NFL commissioner Roger Goodell’s punishments in the Patriots’ Deflategate case underline how inconsistent he has been and the league’s disarray under his watch.

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It’s not the crime that gets you in trouble; it’s the cover-up. That’s what they always say, right?

In the case of Tom Brady and the New England Patriots, they certainly helped increase the size of the NFL’s hammer from ball peen to sledge through their apparent obstruction of Ted Wells’ Deflategate investigation and lack of full cooperation.

But in Roger Goodell’s NFL, I think a new aphorism is in order: It’s not the crime that gets you in trouble; it’s the punishment.

Ever since Goodell took on the role of his pastime’s policeman (not to mention judge and jury), he’s been grappling to find the proper moral tone in his judgments. And, for the most part, failing miserably.

Most of the discussion these days revolves around how Monday’s harsh Deflategate verdict will affect the legacy of Brady. No doubt he’ll never quite shake this incident, and his brilliant career will come with a footnote. But the passage of time will reduce the taint, and it will be Brady’s body of work, not a clumsy deflation operation, that will weigh heaviest in historical opinion.

Ultimately, this whole mess will have more of an impact on Goodell’s legacy — yet another referendum on his power, his judgment, and his seeming flailing hold on the league that pays him $44 million per year to, among other duties, uphold its image.

In using an Uzi to adjudicate this relative mosquito of a crime, Goodell once again showed that compensation for his Ray Rice debacle — a mere two-game suspension prior to release of the video showing Rice punching his fiancee ­— is a never-ending process.

You could see it in Adrian Peterson being suspended without pay for the remainder of last season for “abusive discipline’’ of his 4-year-old son. Also in the 10-game suspension given to Greg Hardy for his domestic-violence case, although Hardy’s guilty verdict on assault charges was dismissed when the alleged victim declined to cooperate.

The NFL’s iron fist didn’t stop there. Cleveland Browns general manager Ray Farmer got a four-game suspension for texting messages to the sideline, and the Atlanta Falcons were fined $350,000 and forfeited their fifth-round selection in the 2016 draft for piping in crowd noise. Team president Rich McKay was suspended for at least three months from the NFL competition committee despite having no knowledge of the event.

And now the NFL has gone hard after the Patriots.

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Yes, it was Troy Vincent, the NFL’s chief of football operations, who technically levied the Draconian punishment: a four-game suspension for Brady, a $1 million fine for the Patriots, and the loss of two draft picks, including a first-round selection in next year’s draft.

But Goodell signed off on it. And though it was Ted Wells who conducted the investigation into how 11 footballs in the AFC title game wound up with air pressure below league standards, it is Goodell who is ultimately responsible for all of it.

And let’s face it, Goodell’s credibility is pretty much shot. It’s not just the Rice incident, from which he may never recover; it’s his seeming scattershot response to the barrage of matters he’s had to handle during his tenure, from the ongoing debate over concussions and player safety to the Peterson incident, Michael Vick’s dogfighting, Spygate and Bountygate.

The overarching impression is that the league is in constant disarray, and Goodell is powerless to stem the tide. He keeps his job because the league is also insanely popular, seemingly impervious to the slings and arrows of persistent scandal.

This particular one isn’t going away any time soon. Brady is lawyering up, having hired noted antitrust attorney Jeffrey Kessler to help with his appeal. Kessler helped get sanctions in the Bountygate case overturned through an investigation by former commissioner Paul Tagliabue, who ruled that Goodell exhibited “selective prosecution” and “selective enforcement.”

Speaking of which, Goodell soon will have to decide whether he’s going to turn over the Brady appeal to another party or serve as the hearing officer himself, which is within his power.

Either choice could lead to potential headaches. If Goodell hears the case himself and reduces the penalties, he subjects himself to charges that’s he’s acceding to the wishes of his old ally, Patriots owner Robert Kraft. If he upholds the verdict, he subjects the league to a further legal battle. And if he lets someone else rule, it will look like Goodell’s authority has waned.

This is not to say Brady and the Patriots are guiltless in all this. You’d have to be naïve to think the quarterback wasn’t involved in some way in the doctoring of the balls — and this organization has a history of pushing the rules to their limit.

But to have Brady’s suspension be twice as long as the one originally meted out to Rice just makes it too easy for critics.

Jimmy Fallon had a good line the other night on the “Tonight Show with Jimmy Fallon.” He said that Brady’s punishment could be reduced if he committed an actual crime.

In Goodell’s NFL, the punchlines never stop coming.