Roger Stone keeps talking about Special Counsel Robert Mueller’s reprehensible behavior with the FBI in Boston way back when.

But I don’t think he or most people understand how bad Mueller’s actions were – “chilling,” is how a Clinton federal judge in 2006 described the former FBI director’s attempts to cover up a massive frame-up by Boston G-men decades earlier.

For the record, Mueller did not railroad four innocent men into prison – two onto death row – for a Chelsea murder they did not commit back in 1965.

That frame job was handled by the Boston office of the FBI, where at one point at least six G-men were taking payoffs from organized crime. That information came from serial killer Stevie Flemmi, who last summer admitted in federal court to taking part in 50 murders.

Everyone knew the four men were innocent, but the FBI wanted them to rot in prison, so the scandal would not be revealed. In the 1980s, two U.S. attorneys in Boston wrote letters to the state demanding that the innocent men not be released, but Mueller, an interim U.S. attorney in 1986-87, did not write one. (At least I couldn’t find one.)

Making sure the innocent men remained in prison was mostly handled by two of the G-men on the mobsters’ payroll, Zip Connolly and John “Vino” Morris, who made sure they left no paper trails. They were hit men with badges — Morris set up a double murder for Whitey Bulger in 1982 in Southie, after which Vino was promoted to director of the FBI training academy in Quantico.

Meanwhile, Zip is doing 40 years in a Florida prison for another gangland hit, in Miami, set up by the same crooked fed who set up the 1965 frame-up.

This is the world of “law enforcement” that Robert Mueller operated in. Not everyone was crooked – just everyone who mattered.

Fast forward to 2006. Mueller is now the FBI director.

After 35 years in the can, two of the four innocent men are dead, the other two have finally been freed. The four men or their estates are suing the feds for wrongful imprisonment. It is not a frivolous lawsuit – they will eventually win a judgment of $102 million.

The plaintiffs – the victims – are trying to get the necessary information from the crooked FBI now run by Mueller about how they were framed. But Mueller absolutely stonewalls the release of the information.

Here’s a show-cause order I discovered last year from U.S. District Judge Nancy Gertner, who presided over the civil case. The FBI was refusing to turn over the exonerating evidence to either the plaintiffs or the Justice Department, which was defending the FBI after its frame up.

Mueller’s stonewalling, Gertner wrote, was a “serious problem.”

“This is a case about, inter alia, informant abuse, about the failure to disclose exculpatory evidence bearing on the innocence of the four plaintiffs, about FBI agents allegedly ‘hiding the ball,’ not disclosing critical information that would have exonerated the plaintiffs, and not doing so, for 40 years.”

Think about that again – for 40 years, ever since the night of the murder, the FBI had known that these four guys were innocent, and yet they never stepped up to identify the real killers, because they were FBI rats. And Mueller’s FBI was prolonging the cover-up, the judge wrote.

“Given those accusations,” she wrote, “the position the FBI is taking is chilling … This Court is not remotely satisfied.”

Six days after Mueller was threatened with contempt, the feds filed this: “This matter has been brought to the personal attention of the Director of the FBI… (the innocent men and the DOJ) have been provided with unredacted copies of the FBI documents.”

And all it took to bring Mueller around to doing the right thing was the threat of a contempt citation by an ultra-liberal federal judge who went to Yale Law School with the Clintons.

Of course, that wasn’t the first time Mueller’s FBI tried to broom the scandal of the four framed men. In 2002, Mueller directed the G-men to oppose state pardons for the four men because the FBI’s own evidence that exonerated them was merely “fodder for cross-examination.”

Despite the FBI’s knowledge that the men, including Peter Limone, were innocent, Mueller’s FBI claimed to a state board that the incontrovertible exculpatory evidence “does not necessarily mean, however, that Limone or any of the other defendants is innocent – it merely means that they are entitled to a new trial.”

By the way, one of the innocent men, Louie Greco, was in Florida the night of the murder he was falsely convicted of. One of the crooked Boston FBI agents (who died in prison in Oklahoma while facing murder charges in another gangland hit) later bragged to a local gangster about their brilliant railroad:

“How does Louie Greco like going from Miami to death row? He wasn’t even there.”

This is your FBI, the organization that Bob Mueller was – and still is – trying to protect from being exposed as irredeemably corrupt.

Good luck, Roger Stone. You’re going to need it, despite your not guilty plea Tuesday.

Howie’s new book, “Kennedy Babylon Vol. 2,” is now available for immediate shipment at howiecarrshow.com.