The Coast Starlight is known across the country as a train ride that hugs the Pacific from California north.
Amtrak train service into and from Boston has been suspended indefinitely over the ongoing marathon bombing investigation.
Mass transit in the city was suspended earlier as part of a city lockdown as police searched for one of the suspects in the marathon bombings.
People waiting for buses and other transit services in Boston were told to head home and stay inside. A no-fly zone was instituted over the Watertown area, the Federal Aviation Administration said. Logan Airport was open but operating under heightened security.
New York City mass transit continues to see heightened security since the marathon bombings, when patrols coverage and bag inspections were increased.
At New York's Penn Station, stranded Amtrak riders trying to get to Boston remained patient.
Lowell, Mass. resident Joe Maloney left Baltimore for Boston Friday morning, but his train was unexpectedly stopped at Penn Station. All the passengers were told to disembark and wait for further instructions.
"I think everyone is understanding and patient," said Maloney. "What's going on up there is more important than what we're traveling for."
The city's mass transit was suspended.
Amtrak is providing updates on train service disruptions on its website.