Team Cuomo’s thundering about fraud as the cause of soaring overtime costs at the MTA has union leaders squawking.

Of course, they wouldn’t be doing their jobs if they didn’t complain when Gov. Cuomo accuses their members of “stealing.”

Notably, the OT surge was highest at the Long Island Rail Road, up 30 percent last year and more than double the 2013 level, the Empire Center reports. And The Post has highlighted some hard-to-swallow extreme LIRR cases, with one guy working the equivalent of 16 hours a day for the whole year.

In all, the LIRR last year racked up $225 million in OT, taking up nearly a third of the $740 million it took in from fares.

But Cuomo’s point man on the MTA board, Larry Schwartz, last week demanded a crackdown on fraud not just at the LIRR, but across the MTA. That has the Transport Workers Union screaming alongside their LIRR brethren. Indeed, the TWU’s head is even making noises about a subway strike.

This, when all the MTA’s labor contracts have expired, though the provisions remain active until new collective-bargaining deals are struck and ratified. And doing anything about soaring OT that isn’t the result of actual fraud will require the unions to agree to major work-rule changes, as the Manhattan Institute’s Nicole Gelinas has outlined in these pages.

But unions always demand to get “paid” for such contract changes, through benefit boosts or higher base pay.

And the last TWU contract gave the union a enormous gift: a guarantee that, if LIRR unions negotiated a bigger raise than the TWU wins, negotiations automatically re-open so the TWU can get a matching pay hike. That is: If the LIRR gives an extra pay hike to “buy” reforms that can rein in legal-but-wasteful OT, the TWU automatically cashes in.

And the LIRR has just 7,000 workers; the subways and buses employ nearly 50,000. This could eat up all the extra revenue the state just found for the MTA, and more.

The governor’s notorious for playing “three-dimensional chess,” with tough talk often concealing his real agenda. For now, we have to just hope he has a real plan here – and that he isn’t just playing it so “clever” that the unions wind up taking him to the cleaners again.

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