Just hours before the so-called “summer of hell” begins at Penn Station, MTA Chairman Joe Lhota again urged Long Island Rail Road riders to “seriously consider” transit options for getting to and from Manhattan as commuters crossed their fingers in anticipation of what awaited Monday morning.

“These are unique circumstances,” Lhota said during a news conference on Sunday at the LIRR’s Jamaica Station. “And part of that, we think, people should look at alternatives. For example, if you work in lower Manhattan, if you work south of Penn Station, seriously consider changing here and going into Atlantic Terminal.”

Starting Monday, Amtrak, which owns and operates Penn Station, will take three of the hub’s 21 tracks out of service for two months from July 10 through Sept. 1. During that period, dubbed the “summer of hell” by Gov. Andrew M. Cuomo, Amtrak plans to make necessary repairs to aging track components at Penn, the nation’s busiest rail station, which serves 300,000 daily LIRR riders.

That construction will result in about a 20-percent reduction in rush-hour trains at Penn — roughly 12 percent during the morning peak hours and 18 percent in the evening peak hours — when trains will either be canceled or rerouted to other terminals, according to the Metropolitan Transportation Authority.

The agency plans to use charter buses, ferries and extended LIRR trains for commuters who can’t practically transfer to subways at other train terminals in New York City, such as Jamaica, Atlantic Terminal or Hunterspoint Avenue.

As the workweek approached, LIRR riders were still fretting over the reality that awaited them.

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“I’m not at all hopeful, [the MTA] can’t keep trains running on a normal day,” said Zack Reed, a stagehand from Seaford who is giving himself an extra 45 minutes to get into the city. “I’m hoping for the best. I’ll be taking my usual train and wait and see what happens.”

Julia Perl, a commercial real estate appraiser from Syosset, said she believes the logistics of the MTA’s service alternatives, unveiled less than a month before the start of construction, weren’t clear enough to instill confidence in her commute.

“I’m expecting significant delays; no one really knows,” Perl said. “It’s not really clear as to what we should expect. Penn is the most convenient option for me. Transferring at Atlantic Terminal could add a half-hour to my commute.”

Amtrak’s decision to tackle the long-delayed infrastructure upgrades at Penn came in the spring, after two derailments occurred at the hub in just over a week.

Sen. Chuck Schumer (D-N.Y.), speaking at a Sunday night news conference near Penn Station, called on MTA and Amtrak officials to “immediately” come to an agreement on spending $430 million in federal funding he helped secure in the aftermath of superstorm Sandy to repair the East River Tunnels. He said the repairs would help the MTA and Amtrak free up funding for other much needed system upgrades.

“This summer is going to be a rotten summer but it can be a little less rotten if they spend this money now and fix up the mess as quickly as possible,” Schumer said. “It’s absolutely ridiculous that when we desperately need money to upgrade the tracks under Penn Station . . . that these two agencies can’t come to a reasonable settlement.”

The track shutdowns this summer will impact service of all three railroads that use the station: NJ Transit, LIRR, which runs the most trains, and Amtrak.

The MTA will make up for reduced service at Penn in two ways: First, it’s tacked on two additional cars to the remaining trains heading into and out of the terminal. Second, the agency has added five new trains at Penn during the fringes of both the morning and evening rush hours, according to Lhota.

The transit chief likened the construction interruptions to superstorm Sandy, which wreaked havoc on the MTA system, saying that agency operations will be similarly coordinated via “war rooms,” or operation centers, to manage commutes and make adjustments when necessary.

“We’re asking Long Islanders who take the railroad to change your habit, to change the way you normally come in,” Lhota said. “But we need to be flexible in our approach.”

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In preparation for the launch of ferry service Monday morning in Glen Cove, the Coast Guard on Sunday worked with local law enforcement to prepare for passenger bag checks and screenings. The MTA plans to run two ferries from the area each morning, one to Manhattan’s 34th Street pier, the other to Wall Street/Pier 11.

Glen Cove officials are using the temporary MTA ferry service as a test for long-term commuter boat routes to Manhattan.

Tom Rowe, 63, of Glen Cove, called the new ferry a “necessary alternative, considering what’s going on with the trains.” He said he is undecided on whether he plans to take the ferry to his Manhattan job early Monday.

Normally, Rowe’s 90-minute commute consists of riding the LIRR’s Oyster Bay line from Locust Valley to Hunterspoint Avenue in Queens and then taking the No. 7 train into Manhattan, where he is a financial planner.

“I don’t think there is any real magic bullet,” said Paul Giulekas, a tax manager from Merrick, who is planning to work an earlier shift in order to continue taking the LIRR directly into Penn Station on his Babylon branch train. “I’m thinking if I go in early enough I won’t have to deal with it — and, who knows? Maybe there will be less people in the office by the time I get there and I could actually get more work done.”

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With Scott Eidler and Laura Figueroa