With the MTA beyond broke, it’ll take fare hikes (and likely more) to keep it running — but New York has little choice, after years of fiscal woes, dubious political oversight by Gov. Andrew Cuomo and high turnover at the top.

On Wednesday, Metropolitan Transportation Authority officials unveiled the depressing options the agency’s considering: Facing billions in red ink over the next years, it’s looking at possible hikes in fares and tolls of 5.5% in 2023 and 2025, service cuts or both. It also wants new revenue streams from the city, state and/or Washington.

The agency’s grim condition was, of course, no secret, but confirmation came from a report Tuesday by state Comptroller Tom DiNapoli, noting that fares would need to rise by 79 cents, or about 29%, to restore revenue to pre-pandemic levels. That’s mainly because ridership is still just 60% of what it was pre-COVID. With soaring expenses and a planned fare hike canceled during the pandemic, riders’ share of costs is now just 32% of the operating budget, vs. 44% back in 2019.

Yet the agency’s been on the wrong track financially for a long time. It declared a similar crisis way back in 2009, leading not only to routine fare hikes but a “mobility tax” for metropolitan-area employers.

Since then, Cuomo for the course of a decade presided over a revolving door of MTA leaders, including Joe Lhota, Fernando Ferrer, Tom Prendergast, Ferrer again, Lhota again, Ferrer a third time, Pat Foye and now Janno Lieber — none of whom, individually, can be blamed for the agency’s chronic crisis but whose collective turnovers, plus incessant political meddling by Cuomo (and, notably, his chief enforcer, Larry Schwartz) surely left the agency with less-than-optimal ability to control costs.

Nor have the politicians let it insist on the kind of union-contract terms for its 72,000 employees that can dramatically streamline operations and contain its $20 billion budget. The result: a never-ending search for “new revenue streams.”

Sure, the pandemic was a fiscal nightmare for transit, with extremely low ridership — and very little fare revenue coming in. But Uncle Sam came to the rescue with $15 billion in aid.

Also true: Many commuters haven’t returned to the system, preferring to work from home or having been scared off by crime. But if that’s going to remain the story for a while, the agency still needs to figure out how to make ends meet.

“For New Yorkers, transit is like air and water,” Chairman Janno Lieber rightly notes. “We need it to survive.”

With the MTA’s contract with the Transport Workers Union up for renegotiation in the spring, the agency will have a chance to lock in better terms — and ensure the union does its part to fill the gap. Beyond that, the city, state and, perhaps even federal officials (Chuck Schumer’s still Senate majority leader) will need to limit the burden on riders — and avoid new taxes. The last thing the trains and buses need is to see people flee not only the system but the state.