As Long Island commuters on Wednesday navigated the third day of the so-called Summer of Hell, Gov. Andrew M. Cuomo once again took to airwaves to cast doubt on Amtrak’s repeated assurances that it would complete its track repairs at Penn Station before Labor Day.

For the most part, both ends of the commute Wednesday were as uneventful as others have been since Monday morning, the first rush-hour commute with the work taking place beneath the bustling terminal. But there was an exception.

The 7 line on the New York City subway — one of the key alternatives for thousands of rerouted LIRR riders who normally ride to Penn Station — was snarled for much of the morning. At one point, a train experiencing “mechanical problems” at Grand Central Station led to the suspension of all 7-line service into Manhattan for about an hour, beginning at around 9:30 a.m., according to the MTA’s website.

Kevin Ortiz, an MTA spokesman, said that LIRR riders had to be diverted to ferries, buses or other subway lines.

“MTA staff worked quickly this morning to resolve a service disruption on the 7 train and to provide alternative transportation options to commuters,” he said. “The cause of the disruption is still under investigation and we apologize for the delay and inconvenience.”

Meanwhile, Charles “Wick” Moorman, Amtrak president and CEO, once again said that his agency, the landlord at Penn, would be able to complete its critical and long-delayed infrastructure improvements by Labor Day. But he left the agency an out: Any work not completed by that time could be wrapped up on weekends, when outages would not impact rush-hour commutes at the nation’s busiest transit hub.

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“If things start to, for some reason, start to look like they’re running behind towards the end, we have the ability to step in at the end and button things up and then finish out whatever we don’t get to in subsequent weekend outages,” Moorman said during a speech at a National Press Club luncheon in Washington, D.C.

Moorman also sought to minimize the likelihood of that possibility. “We’ve done an . . . extraordinary amount of planning on the engineering side. We know we have all the material; we know it all fits; we have everything planned out,” Moorman continued.

But Cuomo, who has been sharply critical of Amtrak, remained skeptical. When asked about Moorman’s comments during a later News 12 Long Island appearance, the governor once again said he had little faith in Amtrak. And once again, he urged the national railroad to turn ownership of Penn Station over to the Port Authority or a private entity.

“Amtrak said it only takes two months, but I take that with two grains of salt. I’m not 100 percent convinced we’re only talking about two months,” Cuomo said. “We have to keep our eye on the ball.”

“The situation at Penn Station is unsustainable, he added. “The LIRR is dependent on Penn and we don’t control Penn. It’s run by Amtrak, and I think that should change.”

Thursday morning will mark the first “Summer of Hell” commute with significant alteration in the MTA’s plan to accommodate Manhattan-bound commuters. After three days of low ridership on charter buses, the agency has cut back on some departures and discontinued service from three of its eight pick up locations on Long Island: the North Hempstead Beach Park, Roosevelt Field Mall and Bethpage State Park locations.

Buses serving the five remaining park-and-rides — at Belmont Racetrack, Nassau Coliseum, the LIRR stations in Valley Stream and Seaford and in Melville — will run every half-hour into and out of Manhattan.

There is also a slight cut in hours of operation. Remaining buses will run every 30 minutes between 6 and 9 a.m., and no longer until 10 a.m. Evening hours, between 3 and 7 p.m., are unchanged.

Bus service for LIRR commuters in Manhattan will also be adjusted to focus on 34th Street, with one stop near Penn Station and a second on the East Side. The MTA will no longer send buses to the area around Grand Central Terminal or other locations along 42nd Street.

“Fewer people are using ferries and buses,” Cuomo said. “It seems people are using the trains to go to diverted destinations. It’s good news.”

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Still, for some riders of the 7 train on Wednesday morning the news was anything but good.

Jessica Ramos, a spokeswoman for Mayor Bill de Blasio, tweeted that she was stuck on a train under the East River for longer than a half-hour, during which she saw fellow passengers “sobbing” over the fear of losing their jobs.

“One of my privileges is to be a salaried public servant,” she said in a tweet. “What about those who are hourly workers & just lost $ to put food on their tables?”