Helena Williams, the first woman president to run the Long Island Rail Road, was fired Wednesday.

After this morning's board meeting, Metropolitan Transportation Authority chairman and chief executive Thomas Prendergast asked Williams to meet him in his office, where Williams said she learned he was replacing her as head of the country's largest commuter railroad.

"I was surprised," Williams, 58, told Newsday in an interview. "I am greatly disappointed. This had been my dream job."

The move comes as LIRR laborers and MTA management remain at an impasse in their nearly four-year-long dispute -- and a potential strike looms.

Williams declined to say why she was let go. She said she believed her firing had nothing to do with the possibility of a strike, pointing out that she is not involved with negotiations.

In a news release announcing her replacement, the MTA said only that Williams was out as president. The agency did not give a reason.

Williams will be replaced by Patrick Nowakowski, a career railroad professional who for the past five years has served as executive director of Dulles Corridor Metrorail Project, which is building a 23-mile rail line to connect with the Washington, D.C., Metro system, Prendergast said in the release.

Nowakowski, 60, starts May 12.

Williams served as LIRR president for nearly seven years, making her the railroad's longest-serving president in decades.

"It's been a privilege to have served as LIRR President," Williams said in a statement released by the MTA. "My focus always has been on providing safe, secure and reliable train service to our customers, and I believe we achieved those goals while improving customer communications and strengthening our relationships with the many communities we serve throughout Long Island. I am deeply grateful to the men and women of the LIRR and to my leadership team who have worked tirelessly to meet the needs of our customers and help modernize the LIRR's operations."

Williams is a lawyer who had served 13 years in other MTA positions, including five years as president of MTA Long Island Bus, before becoming LIRR president in June 2007.

"At the LIRR, Williams improved the railroad's customer communications, oversaw major capital improvements along branches and at terminals, and planned for new service growth while shrinking costs," the MTA said in its news release.

Prendergast thanked Williams "for her long and successful service to the MTA, to Long Island and to everyone in the New York metropolitan region."

He added: "Helena's tireless work to improve the LIRR's operations, communications and community relations has not just made the railroad better for LIRR customers, but has improved the economy and the quality of life for everyone on Long Island."

Kevin Law, president of the business group the Long Island Association, said in a statement that Williams did "an excellent job," and her ouster was ill-timed.

"She was a tireless advocate for the LIRR and the major investments that are being made (and that need to be made) in the system, and given the fact the LIRR is in the midst of major infrastructure projects and labor negotiations, this is a bad decision, bad timing and bad for Long Island," Law said.

Nowakowski had served more than 27 years with the Southeastern Pennsylvania Transportation Authority, Prendergast said, adding that his experience in railroad operations should benefit the LIRR going forward.

"In the coming years, the LIRR must successfully complete the Double Track project along the Ronkonkoma Branch, harden its infrastructure against the threat of future storms, and prepare for East Side Access to revolutionize service," Prendergast said. "Pat's strong background in railroad operations will serve the LIRR well, and I trust Pat to enhance the railroad's operational excellence and emphasize safety and reliability as it confronts new challenges in the coming years."

Nowakowski said he was "deeply honored" to lead the railroad.

"Long Island relies on the LIRR, and Tom has made clear that my job is to make sure the railroad lives up to high expectations every single day, while also planning its future growth to improve the service we provide to Long Islanders," Nowakowski said. "It's a tall order, and I look forward to working with the LIRR's customers, employees and other stakeholders to ensure the railroad achieves its goals."

Jan Burman, president of Association for a Better Long Island, the region's real estate industry group noted that "this change of command comes at a sensitive time for the LIRR and Long Island."

"The rail road is in the midst of crucial labor discussions, it is starting to build a strategic double track from Ronkonkoma and mass transit oriented development is beginning to take place near its stations," Burman said in a statement. "Helena's replacement needs to sustain the confidence the region has come to have in the rail road's progressive efforts while protecting its operational safety and public information initiatives."

Marc Herbst, executive director of the Long Island Contractors' Association, which represents the region's heavy construction industry, praised Williams' work as LIRR president.

"I have worked professionally in the transportation field with Helena for nearly 30 years," Herbst said in a statement. "She has always placed the needs of Long Islanders first. We can be thankful for her outstanding leadership and contributions, and I remain confident she will continue to play a role in the betterment of our region."