A Google Books search for expressions of the form "It's X[,] is what it is" for the period 1940–1975, turned up 20 matches. Nine of those instances set off the "is what it is" portion of the construction with a comma; ten do not; and one uses the construction three times in the same paragraph—once with a pair of commas (to break out a parenthetical associated with the expression) and twice without a comma.
Instances of 'It's X, is what it is'
Here are the examples with comma included.
From testimony of Louis Ferrera in In the Matter of Standard Oil Company of California and Oil Workers International Union, CIO (1950):
Q. Was anything thrown at you at any time during the strike?
A. Yes, I think there was. I was standing at 16 Gate, I recall it now. There was a guy in there, it was a sedan, what kind of car it was I don't know, but there was a 12 inch crescent thrown out out, and it just missed me by inches.
Trial Examiner MYERS. 12 inch what?
The WITNESS. 12 inch crescent.
Trial Examiner MYERS. What is that?
The WITNESS. Regular wrench they use for taking nuts and bolts. It's a machinist's wrench, is what it is.
From "Testimony of Adolph Van Cura," in United States of America V. Rabin (1962):
Mr. Gorman: Would you give me the name of them [the six bonds] again, please?
The Witness: Dominion of Canada.
Mr. Gorman: And any particular issue?
The Witness: Due September 6, 196— Well, it's Ninth Victory Loan, is what it is.
From Mel Jones, "Recon All the Way," in The Leatherneck (October 1963):
Such are the jobs of Force Recon. and a couple of the methods they employ. What's left now? The image.
An image, according to the Madison Avenue crowd, is that impression which you project upon the public. Shucks, it's your reputation, is what it is.
From "Charge of the Court to the Jury," in Sias v. General Motors Corporation (1964):
THE COURT: ... I know of no better definition [of exemplary as used in the legal term "exemplary damages"]. I don't think there is a better one. I looked in Webster and the one that came closest is "serve as a warning or deterrent but not as punishment," in other words, a matter of degree of which, if you feel that the facts warrant it, will allow you to go, award in excess of actual damages bur not such a great amount that they would constitute punishment. I know of no other way of saying it. It's a vague subject. It's within your good sound judgment, is what it is.
From "Testimony of Leonard Hutchison," in the Warren Commission, Investigation of the Assassination of President John F.Kennedy (1964):
Mr. HUTCHISON. This is a friendly store, Mr. Jenner. It's not a cold store—like a chain-store or anything like that. We don't change help and it's just a—well, it's a neighborhood supermarket, is what it is.
From "Testimony of Edward Gorman," in Baldinger v. Ann Arbor Railroad Company (1964):
Q. And when that [oil base] leaks out you're going to have a hot box; is that true?
A. Well, I wouldn't say it leaked out. It's just oily waste, is what it is.
From an unidentified panel discussion in The Pacific Reporter (1967) [snippet view]:
Conn: There's another approach to this too, also, especially on a guilty plea, is the court will ask the District Attorney as to your attitude and you understand our penal system is not a punishment system, it's a rehabilitation plan, is what it is, based on this idea.
From "Interview: KIIS-AM Format to Be Rewarding," in Billboard Magazine (November 25, 1972):
[CHUCK] BLORE: People are just too logical to accept a sound or a word or a voice without it having an additional meaning to them. If they hear a voice it's got to have a body. And they don't do it consciously. I long ago rejected the "theater of the mind" concept. It's the theater of the gut, is what it is.
From an unidentified interview in The Canadian Forum, volume 53 (1973) [combined snippets]:
BK: You see the two trends going on simultaneously?
CC: Yes I do, and I also see that it is not all bad. In many cases, in the local art schools, the teachers were very mediocre painters. People who were not open to things at all. That was the case of the Ontario College of Art when I was there. So that what happens is a more open attitude comes in, in a way, but at the same time it is closed. You know what I mean, it's a jump from one form of provincialism to another, is what it is. And there is never any real local identity involved.
Instances of 'It's X is what it is'
Here are the ten instances that omit the comma.
From testimony of Charles Riffle, in Hearings of the U.S. House of Representatives Armed Services Subcommittee (1955):
Chairman PRICE. You mean that the school district at Shore Acres received funds from the Federal impact program?
Mr RIFFLE. No, the entire school district; Shore Acres is not a school district. It's the Mount Diablo Unified School District is what it is.
From testimony of Stanley Younce, in "Report of Subcommittee on Mine Safety in Metallic and Nonmetallic Mines," in Hearings (and Report) Before the U.S. House of Representatives Committee on Education and Labor (1956):
Mr. FJARE. And they [attempts to correct "deplorable working conditions"] have failed?
Mr. YOUNCE. Well, there might be some better conditions, but our immediate department hasn't changed any at all. Now, some departments, they say, have eliminated most of the dust—but like I say, you are going to have some dust and some gas, it's a smelter is what it is; but I think a lot of it could be eliminated.
And from Ira Levin & Mac Hyman, No Time for Sergeants (1958):
WILL. ... Sergeant King, though, he come out on top. He did. The instructors said they never seen nothin' like it. It was just as if he had copies of the tests before they give them. He done so good that General Bush—he's kinda like the principal of the school—General Bush give him his stripes back and made him his orderly, and an orderly is kinda important; it's like a right-hand man ... or an assistant ... or a helper.... Well, it's really more like a servant is what it is.
From Lanford Wilson, The Rimers of Eldritch (1966):
WILMA. A show place. (Martha and Wilma sit. Lights come up on upper top platform and the Johnson family "kitchen"—Mavis, followed by Patsy—R.—L.)
PATSY. It's a trash heap is what it is.
From "Testimony of Merle Williamson" in Illinois State Journal-Register, Inc. V. National Labor Relations Board (1968):
A. I don't know of anything [highly confidential]. I don't know how you can designate which is more confidential than any other.
Q. In other words, it's just a list of customers is what it is?
A. Yes.
From From H.C. Greisman, "Social Movements and Mass Society: Requiem for the Counter-Culture," in The Substance of Sociology: Codes, Conduct, and Consequences (1973), citing a cartoon by R. Crumb, Plunge Into the Depths of Despair (1970):
But the full force of criticism has come from middle class young people who make up most of the counter-culture. The sarcastic lamentations of Robert Crumb are typical:
It's really too bad, the way things worked out ... it could've been so beautiful! What's the modern world coming to? It's not much fun but it's efficient. It's neurotic is what it is! Millions of desperate consumers roam the streets of large cities, trying to find some unknown ego fulfillment. And the more crowded it gets, the more cut off they are from one another ... real experience is replaced by fantasy. The individual is rendered helpless by impossible longings ...
From an unidentified story in Esquire Magazine, volume 75 (1971):
"Hogarth, you are a maniac," said a boy in a nearby desk, at once affectionate and condescending.
"Well, but it's true, you know,” continued Hogarth, warming to his theme. "You see, the whole thing is this. That crummy monk, you see, is a sort of transvestite-type person. It is a kind of psychiatric case is what it is.
From an interview with Father Daniel Lyons in The Top of the News with Fulton Lewis III (1971) [combined snippets]:
LEWIS: "Father Daniel Lyons, some say this is a religious war in Northern Ireland—Catholic versus Protestant. Some say it is an economic war—the poor against the rich. And some say it's a political war—the leftist rebels against the right. In your view, what kind of war is it?"
FR. LYONS: "Well, you know, it's political opportunism on the part of the Unionist Party is what it is. Normally, in a democratic system, you have a Labor Party of some kind, working people get together, and then you have a middle class and upper class party, so to speak, and these may cross lines. But basically you have—you try to prevent abuses from either side. ..."
From "Drug Abuse," in Navy Supply Corps Newsletter (April 1972):
QUESTION: Could you explain it [the experience of a bad LSD trip]?
ANSWER: It's terrifying is what it is. It's the most scariest thing you ever had happen to you. That's what it is. It's the most terrifying experience I had in my life.
From Stuart Bauer, "The Long-Playing Widespread Supermarket Check-out Counter Rip-off," in New York Magazine (September 2, 1974):
Of course, it's as crooked as hell, what you're thinking, he thought, jumping up. It's criminal from the word go is what it is, he thought, no getting away from that . . . Unfortunately, it's foolproof.
An instances that includes a comma in one sentence and omits it in another
One source handles the expression with a pair of commas once and without a comma twice in the same paragraph. The pair of commas serves to break out a parenthetical observation, however, so the author's punctuation in that case is arguably not inconsistent with his punctuation of the other two.
From Dow Mossman, The Stones of Summer: A Yeoman's Notes, 1942-1969 (1972):
"Yes, sir, Dawes," Abigail Winas said in other summers, sitting alone within her thick hennery of fox grass, carving on chickens, "it's exactly like that French skull you dug near the river with that old set of junked spoons. It's mostly dead and not swarming beyond itself is what it is. This valley is. It's damn history, and not much of that, is what it is. It's dire is what it is," she said, laughing, "just dire's hell."
Discussion
Although I ran searches for the period 1940 to 1975, the earliest match for "It's X[,] is what it is," the earliest match that Google Books returned was from 1950. I ran a followup Google Books search over the period 1900 to 1949 and found no matches for the construction.
In looking for a pattern in the two sets of results, I speculated that the number of words in the X component in the construction (where X is the wording separating "It's" from "is what it is") might be longer in instances that included a comma than in instances that didn't—but that doesn't seem to be the case. The number of words in the X component of the nine instances that included a comma were 3, 3, 2, 5, 3, 3, 3, 5, and 9; while the number of words in the X component of the ten instances that omitted a comma were 6, 2, 5, 3, 5, 1, 5, 9, 1, and 5. The instance that included paired commas in one sentence and omitted a comma in two others had X values of 7 words, 7 words, and 1 word, respectively.
Perhaps the strongest indicator of whether a comma would be included is whether the writing was done in a legal proceeding. Four of the five instances from courtroom testimony include a comma, as does the only instance from a law journal. On the other hand, of the three instances involving Congressional testimony, only one includes a comma.
Overall, it would be hard to find a more even split than the one in these examples from the period 1950–1975 between "It's X, is what it is" and "It's X is what it is." Consequently, you can point to numerous examples in support of whichever form of punctuation you prefer.
