A file photo of Joseph Lhota at a City Hall...

A file photo of Joseph Lhota at a City Hall news conference. (May 23, 2000) Credit: AP File, 2000

Joseph J. Lhota, former Mayor Rudy Giuliani's second-in-command during the 2001 terror attacks on the World Trade Center, has been chosen by Gov. Andrew M. Cuomo to head the nation's largest public transportation system.

Lhota, 57, of Brooklyn, will take over as chairman and chief executive of the Metropolitan Transportation Authority, pending confirmation by the State Senate. Lhota, who was deputy mayor of operations and city budget director under Giuliani, replaces Jay Walder, whose last day at the MTA was Thursday.

"Joe Lhota brings one-of-a-kind managerial, government and private-sector experience to the job and a lifelong commitment to public service that will benefit all straphangers," Cuomo said in a statement. "I look forward to working together as we continue to reform the MTA, reduce costs and improve service for New Yorkers."

Lhota, who grew up in Lindenhurst and graduated from St. John the Baptist Diocesan High School in West Islip, is executive vice president of administration for The Madison Square Garden Co. Before his current post, he had worked since 2002 in executive positions at Cablevision, which owns Newsday.

The presumptive MTA chief will take the post during a volatile and difficult time for the agency, which runs the Long Island Rail Road, Metro-North Railroad, the New York City subway and bus system, most of the city's toll bridges and tunnels, and Long Island Bus. Budget shortfalls in recent years have neared $1 billion, and in 2009 the State Legislature had to craft an unprecedented bailout to avoid huge fare hikes and deep service cuts. The bailout included fare increases in 2009, 2010 and 2013, and a controversial payroll tax on businesses in the MTA's 12-county service area.

The agency plans to borrow heavily to continue to pay for huge capital endeavors -- including the LIRR's East Side Access project that will bring riders to Grand Central Terminal, and the Second Avenue subway. It is looking for big givebacks from unions during upcoming negotiations.

In a statement, Lhota said that throughout his career he has "initiated reforms that are performance-based and that cut costs" and that he aims to do the same at the MTA.

Mark Epstein, LIRR Commuter Council chairman, said he hopes Lhota, as a former Long Islander, "understands and values the needs that the Long Island Rail Road has."

New York City Mayor Michael Bloomberg, in a statement, called the MTA's top post a "daunting challenge," but said Lhota has the "talent, skill and experience" for the job.

"The MTA has serious problems that have to be confronted head-on," the mayor said, "most notably the absence of a dedicated, reliable mass-transit funding stream to rebuild the system and give New York City the 21st century transit system we deserve."

Lhota joined Giuliani's team in 1993 after working for 15 years as an investment banker. He earned his master's degree in business administration from Harvard University and bachelor's in business administration from Georgetown University in Washington, D.C.

Giuliani called Lhota an excellent manager who "ran the city" for years as his top deputy. Giuliani said Lhota was the first person he saw when he arrived at Ground Zero following the Sept. 11 attacks, and that Lhota was at his side as he managed the crisis for the following four months.

"He's a very good executive. He knows how to organize people. He knows how to motivate people," Giuliani said. "He has both the substantive intellectual background for the job, and he has the personality for it."

Mitchell Moss, director of the Rudin Center for Transportation Policy and Management at New York University and a member of the governor's search committee for the next MTA chairman, said Lhota's background in city politics and finance make him the right MTA boss for the times.

"We have people who know how to run the railroads," Moss said. "We need someone who knows how to manage the money and the debt."

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