Bobby Baker, the former Senate aide who went to prison in a scandal of the 1960s turned up in U.S. Tax Court yesterday in a campaign of self-vindication that he says is doing amazingly well.

"They had $1.3 million in claims against me back in 1972 when I got out of prison," he said. "But I've just been beating the hell out of them. I've got 'em down to about $200,000 already."

Now 48, Baker waited in a back row of Tax Court Judge Walter Goofe's courtroom yesterday afternoon for a case involving the Internal Revenue Service and an old friend of Baker's, Seymour Pollack, who is also being chansed for back taxes after a prison term for stock fraud.

Goffe listened patiently as Pollack, representing himself complained of a mysterious theft from Baker's basement sometime after Baker began serving a 1-to-3-year prison term in January, 1971.

Boxes of documents, some Pollack's and some Baker's, were stolen, Pollack charged, only to end up in government files. A former New Jersey stockbroker convicted of stock fraud here in 1973, Pollack charged that they were stolen by the government." He pointed an incriminating finger at a woman who used to be first his secretary and then Baker's. Pollack then offered the court a couple of Internal Revenue Service document indicating that the woman was one of its informants.

Moving to call Baker as a witness, Pollack charged as he has before in the federal courts in New Jersey that the basement theft and other improprieties were all part of a Nixon administration plot to "get Baker and probably through Baker, to get Larry O'Brien," the former Democratic national chairman whose offices were burglarized in the Watergate scandal.

Judge Goffe sent the entire tax case back to the U.S. courthouse in Neward, whence it came, for further proceedings. The IRS lawyer at the hearing, William Gross of Neward, allowed that "there probably was a theft of documents from Mr. Pollack and perhaps Mr. Baker," but Gross insisted that "the government had no knowledge of that."

Microfilmed copies of some of the stolen papers were first revealed in 1976 in the possession of the Justice Department's strike force in Newark. The disclosure was made during pretrial discovery proceedings concerning another criminal indictment against Pollack that was subsequently dropped.

"It was a very fine black bag job," Baker said. The thieves, he explained, made off with the juicies documents in the basement, including embarrassing information about presidents and lawmakers.

Chuckling enthusiastically despite his being passed over as a witness, Baker voiced confidence after the hearing that Pollack's efforts, along with litgation of his own, would eventually produced enough evidence to win Baker a new trial.

"He [Pollack] gets all this stuff free and I'm laughing all the way to the bank," Baker said cheerfully of his successes thus far in beating down post-prison tax claims.

Now engaged in a real estate business, Baker was convicted in 1967 of larceny, fraud, conspiracy and attempted tax evasion, but he maintains the jury found him guilty because it felt he was lying about the transactions in question. The government's files, he contends, will eventually show that he wasn't.

Still more will come out, Baker hinted, with publication of his memoirs in June. Originally the book was to be called "Child of the Senate," but the final title is catcher: "Wheel Capitol Hill Operator."