Joseph Lhota, returning chairman of the Metropolitan Transportation Authority, said Thursday he is ready to lead the LIRR through its so-called summer of hell, even if it means heating up the simmering feud between the MTA and Penn Station’s owner, Amtrak.

“Bring it on,” Lhota, 62, said in an interview with Newsday, a day after his surprise same-day nomination and late-night confirmation by the state Senate as head of the largest public transportation system in the nation.

Lhota made it clear that he has no intention of backing down from the MTA’s vow to go after Amtrak for the costs the LIRR will incur this summer mitigating the construction-related service disruptions at Penn Station — even if it means withholding tens of millions of dollars in funding to Amtrak.

Lhota said the emergency repairs at Penn this summer “are nothing more than the accumulation” of 40 years of neglect by Amtrak. And, despite Amtrak and MTA Board members warning against a prolonged legal battle between the two rail providers, Lhota said he’s up for the fight.

“They’re like a bully in a schoolyard,” Lhota said of Amtrak. “And I’m a big enough guy to look at some bullies and say, ‘It’s not going to happen anymore.’”

Lhota, who sat on the task force empaneled by Gov. Andrew M. Cuomo to come up with solutions to the problems at Penn, stood by the MTA’s transportation strategy to move commuters this summer, which includes supplementing LIRR trains with ferries and buses. However, Lhota said, the authority would have to be “flexible” and evaluate the plan as the summer progresses.

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“To make the trip into New York City as effective and efficient as possible — that’s the goal. And we’re going to move heaven and earth to meet that goal.”

Lhota said, in the long-term, solutions to the LIRR’s commuting crisis will come in the MTA’s capital program, which includes billions of dollars in investments in modernized signals and positive train control technology, and in moving ahead with plans to renovate and beautify Penn Station.

Lhota said one good thing that could come out of this summer’s service disruptions is a realization by some customers that there are alternatives to commuting to and from the dilapidated, century-old Manhattan train terminal. Those could include permanent ferry service and increased use of the LIRR’s other terminals in Queens and Brooklyn, Lhota said.

The former Lindenhurst resident also weighed in on other issues facing LIRR commuters.

He said the LIRR’s $2 billion plan to build a third track between Floral Park and Hicksville is “critical to the economy of Long Island,” and that opponents have yet to raise a good argument against it.

Lhota said he also still believes that East Side Access project to link the LIRR to Grand Central Terminal will be “great” when it’s finished, but recalls the constant delays and budget overruns having “frustrated me to no end” during his first stint as MTA boss between 2011 and 2012.

Lhota said although he originally had no interest in returning to the authority when the job opened up in January, he was won over by the prospect of the MTA chairman and executive director roles being split, making his a part-time job. Lhota, who holds a leadership role at the NYU Langone Medical Center, said he plans on surrounding himself with a strong team that will run the MTA day-to-day. And, Lhota said, he’s “comfortable” with Cuomo’s increasingly hands-on oversight of the agency.

“I will, under all circumstances, be held accountable for everything that happens at the MTA,” Lhota said. “I’m willing to accept that.”