MTA Long Island Rail Road president Helena Williams speaks while...

MTA Long Island Rail Road president Helena Williams speaks while on the train platform after a news conference at the Port Washington LIRR station in Port Washington, Nov. 15, 2013. Credit: Steve Pfost

Ousted LIRR president Helena Williams' criticism of a Gov. Andrew M. Cuomo-backed MTA plan to link Metro-North Railroad to Penn Station -- potentially inconveniencing Nassau and Suffolk commuters -- cemented her reputation as a fierce advocate for Long Island, but it also contributed to Williams losing her job, sources said.

Williams, 58, whose seven-year stint as Long Island Rail Road president ended Friday, clashed with Metropolitan Transportation Authority chairman Thomas Prendergast over the Penn Station Access project, which would bring Metro-North into the LIRR's West Side Manhattan terminal using existing Amtrak tracks around the same time the LIRR would connect to Grand Central Terminal as part of East Side Access, sources said.

"There was definitely a rift over that," said one MTA source who spoke on condition of anonymity. "Tom seemed to be on the side of pushing this thing forward, and his agency president was not. She was sort of pulling in the opposite direction."

"I don't think there's any question that it helped her demise," MTA board member Mitchell Pally said.

Praised for service

Williams declined to comment. Prendergast would not address the Metro-North project issue, but in a statement praised Williams, the first woman to run the nation's largest commuter railroad, for making the LIRR "better for everyone who relies on it."

"She always saw the railroad from a customer's perspective, and always urged the railroad to improve how it served and communicated with its customers," Prendergast said.

Patrick Nowakowski, 60, a veteran Philadelphia and Washington, D.C., transit executive picked by Prendergast to replace Williams as LIRR president, takes office Monday.

Although Williams has said she supported bringing Metro-North to Penn, she repeatedly expressed reservations inside the MTA on how it would affect the LIRR, which she feared could be forced to reduce service to the station to accommodate its sister railroad, sources said.

She supported efforts to expand capacity at Penn Station -- including by building new tracks there -- before inviting a fourth railroad into the nation's busiest train station, already used by the LIRR, Amtrak and New Jersey Transit.

Eight state lawmakers from Long Island expressed similar concerns when they wrote a letter to Prendergast's predecessor, Joseph Lhota, in 2012 urging him to drop the project, which the state comptroller's office in 2008 estimated will cost $1.2 billion. The MTA has said it will cost $516 million.

Long Island's Republican state delegation -- led by then-Senate Transportation Committee chairman, and Williams' political ally, Charles Fuschillo -- also held up Prendergast's Senate confirmation as MTA chairman for months last year until they received assurance from Prendergast that the LIRR would not be impacted by the project.

"To the extent that he [Prendergast] held that against Helena Williams, as misplaced as that is, is unfortunate," said Sen. Jack Martins (R-Mineola), who vowed to continue fighting against the project in Williams' absence. "If they can't do it without displacing the Long Island Rail Road, then they can't do it."

Prendergast, responding to Martins during his Senate confirmation hearings, vowed that the LIRR would keep all 37 of its morning rush-hour slots in Penn Station. But when Cuomo mentioned the Penn Station Access as a top transportation priority in his State of the State address in January, his spokesman said the LIRR could afford to reduce service at Penn because it would be gaining slots at Grand Central.

'Just being parochial'

The project got another boost when Cuomo and the MTA made it the centerpiece of a $5 billion application for federal Sandy resiliency funding.

A Cuomo spokeswoman did not respond to a request for comment. "I think people looked at that and said it's all well and good to be pro-Long Island, but you can't say, 'We're going to run 40 percent of our service into Grand Central but we're going to still need every piece of real estate over at Penn,' " a source said. "I think people looked at it and said, 'She's just being parochial here.' "

But Pally, of Stony Brook, who shared Williams' concerns over the project, said her firm stance on the subject is what made her a "tremendous" Long Island Rail Road president.

"She understands that the first two words of that title are 'Long Island,' " said Pally, who believes Williams knew the potential ramifications of her dissent on the project.

"There are very few people on Long Island that have more credibility than Helena Williams, and part of that is because she's willing to say . . . 'This is not good for Long Island,' " he said.

Fuschillo, who resigned from the Senate in December to become chief executive officer of the Alzheimer's Foundation of America, agreed that Williams was a "true professional" and an "advocate for all of Long Island." He called her ouster "a tremendous mistake."

MTA board member Charles Moerdler -- a strong proponent of the Penn Station Access project, which would provide new Metro-North service for his home community of the Bronx -- said he doesn't believe Williams' reservations were a "significant factor" in her termination.

"We didn't see eye to eye . . . We disagreed most agreeably and never had harsh words on it," said Moerdler, who believes the project could be accomplished without inconveniencing LIRR riders. "She had a point of view, and that point of view was not unreasonable . . . I have a different point of view."

In February, the MTA said it was working on a federal environmental assessment for the project and expects to have all governmental reviews of the effort complete by 2017. According to MTA documents, Metro-North would run as many as 10 trains an hour into Penn on weekday mornings.

MTA's Penn Station Access plan

INFRASTRUCTURE: Metro-North Railroad would link to Penn Station on its New Haven line mostly using existing Amtrak infrastructure, including tracks across the Hell Gate Bridge. Four new Metro-North stations would be built in the Bronx.

COSTS: The MTA has said the plan will cost $516 million. In 2008, the New York State comptroller estimated the cost at $1.2 billion.

RIDERSHIP: The MTA has said it would run 10 Metro-North trains an hour into Penn and bring as many as 28,000 new customers there. Penn Station is now accessed each weekday by about 500,000 passengers using the LIRR, Amtrak or New Jersey Transit.

REGIONAL PLAN: The new service would begin around the same time that the LIRR would begin running trains to and from Grand Central Terminal as part of East Side Access, which federal officials expect will be completed in 2023.

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