MTA Chairman Thomas Prendergast is stepping down after nearly 30 years at the agency where he built a reputation as a ‘‘tough negotiator’’ who modernized the Long Island Rail Road and completed the first phase of the Second Avenue Subway.

Prendergast, 64, will retire in early 2017, Gov. Andrew M. Cuomo announced Monday. Prendergast’s Metropolitan Transportation Authority career has included stints as president of the LIRR and NYC Transit, and MTA chairman and CEO since June 2013.

“Tom Prendergast has overseen the re-imagining and modernization of the MTA and will be remembered for improving the commute, and the lives, of millions of New Yorkers,” Cuomo said. Now, ‘‘he has some personal issues and some family issues that he needs to deal with.”

The governor did not say who would succeed Prendergast. Spokesmen for Cuomo and the MTA declined to discuss speculated potential choices.

Cuomo said, however, they have a couple of weeks to find a replacement, and that the person has to be “an operator of the transit system who . . . is also a developer.” Cuomo’s nominee will be subject to confirmation by the State Senate.

Mark J. Epstein, chairman of the Long Island Rail Road Commuter Council, said Monday that Prendergast has always been open to discussing riders’ concerns about the railroad’s performance and building plans.

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“It is our hope that whomever his replacement is brings with them the view that this is first and foremost a rider-based system, and the needs of the commuter must figure into every decision that is made,” Epstein said.

When they first discussed the MTA chairmanship, Prendergast agreed to oversee the agency for about three years, Cuomo said Monday at his midtown offices.

“The MTA is probably one of the toughest jobs in the state, it is every day, it is 99 percent bad news,” Cuomo said. “It’s not a lot of good news coming to you when you’re the MTA chairman, except the Second Avenue subway.”

Cuomo appointed Prendergast to the post on an interim basis as of Jan. 1, 2013, and he was confirmed by the State Senate on June 20, 2013. His term would have expired June 30, 2021.

“Opening the Second Avenue Subway this weekend was a crowning achievement for the MTA and I’m proud to have been a part of such a historic moment,” Prendergast said in a statement. “It has not only changed the daily commute for hundreds of thousands of customers, it has helped change the face of the MTA — showing the public we can meet the deadlines we set for ourselves.”

Prendergast, a resident of upstate Brewster, became president of the LIRR in 1994 and was credited during his six-year term with modernizing its aging diesel fleet, introducing more durable concrete rail ties and modernizing onboard air-conditioning systems.

To ensure “we don’t lose any momentum with the third track, East Side Access tunnel and the new Penn Station projects,” Cuomo should nominate someone with commuter rail experience “in addition to the traditional urban bus and subway management experience,” said Kevin Law, president of the Long Island Association, the region’s largest business group.

Members of Long Island’s state Senate delegation on Monday praised Prendergast’s attention to the LIRR, both as MTA chairman and previously as railroad president.

They cited his successful efforts to secure funding for building projects, such as East Side Access to bring the LIRR to Grand Central Terminal and the Double Track project between Farmingdale and Ronkonkoma.

State Sen. Carl Marcellino (R-Syosset), co-chairman of the Senate transportation committee, said Monday he hopes Cuomo’s nominee will understand the LIRR’s needs differ from those of the New York City subways. “You need someone who is conscious of that and is willing to work with local governments and elected officials along the way; Prendergast did that.”

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Marcellino and outgoing state Sen. Jack Martins (R-Old Westbury) praised Prendergast’s “blunt, direct and straightforward” style. “He’s a tough guy, a tough negotiator . . . I appreciated his directness,” Marcellino said.

Martins, a member of the Senate transportation committee, opposed Prendergast’s drive to add a third track on the LIRR from Floral Park to Hicksville, but lauded his stewardship of the MTA. The senator also said commuters would benefit from the building funds secured by Prendergast for years to come.

“Sometimes we looked at things a little differently, but I think overall he has been a positive for the MTA,” the senator said. “I’m sorry to see him go.”

With Emily Ngo