The track work at Penn Station is supposed to last throughout the summer until September 1.
The repairs will improve reliability, but they won't add capacity or ease overcrowding at Penn Station.
Trump has proposed eliminating a grant program that was to pay for half of the tunnel project, which is now estimated to cost about $13 billion.
New York City rail commuters have gotten through their first morning with modified schedules while Amtrak begins extensive repairs in Penn Station prompted by two recent derailments and other problems. "I wasn't able to get a seat", said Kate McMillan, 64, who travels into the city from Plainfield, New Jersey.
He says the 7:23 train from Mt. Instead, the most noticeable inconvenience that Boston-based users of Penn Station might notice is more crowded Amtrak trains.
New Jersey Transit is also changing the routine for its customers who ride North Jersey Coast Line trains to Hoboken Terminal.
Lex Marshall of Morristown says there's a lot of confusion and too many people gathered in one space. "Everybody's just bumping into each other, pushing each other, to get to their destination".
"The test - the second piece of this is tonight", said Charles Ingoglia, an NJ Transit spokesman said.
Dubbed the "summer of hell" by commuter-beloved Gov. Andrew Cuomo, Amtrak has begun major station track renewals and signalling switches updates-long-awaited emergency repairs needed at the country's busiest transportation facility.
The construction is due to stretch until early September and some New Jersey commuters are facing the decision of how they will face their new routes.
Nick Sifuentes, the deputy director of the Riders Alliance, said Monday morning's commute was largely fine, but he's more concerned about what happens when everything doesn't go according to plan.
In response to the issues, PATH is adding enough trains so that one will arrive every five minutes.
"I rode the train this morning to see first hand the effect summer fix work is having on commuters", said Guadagno in a statement.
In a survey aimed at illustrating the financial hardship caused by the city's subway system, almost 75 percent of respondents blamed trains for their late arrival at work during the last three months, while 13 percent said they'd been docked wages.
"The ferry is a stress-free commute because it's a guaranteed commute, it's a 99 percent on-time performance we have", said Jennifer Schuck, from the New York Waterway.
Amtrak's plan for the accelerated work came after two trains derailed at Penn Station in less than two weeks this spring.
"Compared to Europe, I feel like we're living in the Third World", said Mark Van Wagner, an artist and art dealer who takes the Long Island Rail Road from Bellport, New York.
But he conceded that the evening rush could be more dramatic, as commuters tend to travel out of the city in a tighter time window.