A s he wrapped up the legislative session Friday, Gov. Andrew Cuomo crowed that it had been the “most productive” in history. Indeed — for him. With lawmakers distracted by hot progressive issues, he essentially stole the Metropolitan Transportation Authority. Now, it can’t be denied that Cuomo ­really owns the MTA.

Since Cuomo got congestion pricing passed in April, he has been conspicuously quiet about the state-subsidized MTA. The governor didn’t even mention it in his “list of accomplishments” last week.

But the unwieldy bill that lawmakers had passed in the early-morning hours wasn’t silent.

First, the legislation creates a new “director of transformation” for the MTA. This sounds like a person in charge of Cirque du Soleil costumes, but the person — identity unknown, at the moment — will carry out the biggest, er, transformation that the MTA has ever seen in its 51-year life: a complete “personnel and reorganization plan,” including, possibly, getting rid of entire divisions, such as the one that runs the subways.

The MTA could maybe stand some transformation, but this is a huge task: changing what 70,000 people do, overnight.

And now, it will be a one-person job. By July 30, the MTA’s supposedly independent board “shall approve” the transformation plan.

There is no word on what will occur if the board doesn’t exercise its theoretical free will to vote “no,” or if the board doesn’t think the plan that consultants are cooking up now is worthy of instant approval. Once the plan is approved, the MTA board will appoint this Transformation Man (or Woman).

And from there on in, Transformation Man will report directly to the board — not to the MTA chairperson. That creates a bizarre chain of command.

It makes the person far more powerful, for example, than, say, subways chief Andy Byford, who was sold to the public, nearly two years ago, as an expert given a great deal of independence and autonomy to fix the subways.

But at least we have the board to offer some resistance, right? After all, Cuomo appoints six members (including the chair). The city gets four.

Yet last week’s legislation tips the balance even further in the governor’s favor.

Cuomo got lawmakers to waive a downstate “residency law” so that his state budget director can serve on the board. His other new appointee is his financial-services chief.

So now one-third of Cuomo’s appointees are direct state employees in their other jobs — hardly making them paragons of independence.

And the city, right now, only has three board members. As ­Politico reports, Cuomo failed to send one of Mayor Bill de Blasio’s recent appointees, climate adviser Dan Zarrilli, for a state Senate vote, claiming he needs a criminal-background check. Zarrilli is a longtime government official who doesn’t appear to be living a secret life of crime.

So it’s six against three — and don’t expect the people who represent suburban counties on the board to pick up the slack. Their county budgets are beholden to the state and thus to next year’s state budget.

It’s a bad precedent for the Legislature to allow all this. And now, with his budget director as an “ex-officio” MTA board member — that is, someone who serves automatically on the board, by virtue of his other government position — it’s theoretically possible that Cuomo could delay other, future board nominees, letting the board dwindle down to, well, his.

Lawmakers should have considered all pending board nominees or none at all.

Cumulatively, the Legislature’s votes last week ensure that lawmakers get no real say going forward on the MTA’s biggest change in history.

What about other checks and balances? The real-estate industry isn’t without its sins, but it has always served as an important voice sticking up for transit. In refusing to even discuss tighter rent regulation with the industry before signing it into law, Cuomo sent the industry a clear message a week earlier that will help him on MTA ­issues, as well: Stay away — or else.

Finally, there’s our missing mayor. An activist, or even slightly sentient, mayor could have instantly recognized the ominous nature of these changes, and lobbied city-based state legislators to think first. Instead, our mayor was preparing to spend another weekend out of town.

Nicole Gelinas is a contributing editor of City Journal.