The LIRR and Amtrak restored full service to the evening commute after track repairs.
The train from Huntington due in at Penn Station at 7:17 was stuck in the tunnel for over an hour, according to Eyewitness News reporter Josh Einiger.
LIRR says 1000 people were on the train. They had been on backup power, which means dark lights and possibly no air conditioning. Train crew gave out water, LIRR says.
Crews pushed the stuck train with a diesel rescue locomotive to the Hunter's Point Station in Queens
As LIRR rescued its stranded passengers, tens of thousands of Monday morning commuters were inconvenienced as well, as the railroad consolidates and cancels trains to account for one fewer tunnel.
Up to 15 LIRR trains were cancelled or combined.
At the peak of the problems, delays up to an hour were reported going westbound. Trains were reported on or close to schedule in and out of Penn Station shorty after 11:00 a.m. - too late for many frustrated commuters.
"I'm supposed to be in the office at 9 and this isn't the first time," Connie Kalimullah, Copiague resident, said.
"I've flown to Florida in less time than it took to get in this morning," David Horvath, Long Beach resident, said.
Every month this summer, there has been some sort of major issue in one of the East River tunnels, stranding thousands of passengers
Amtrak says more than 90 percent of the time passengers going in and out of Penn Station get there on time.
"I hear horror stories all the time I travel into Manhattan, Brooklyn and there's a glitch here and there. It's technology. Stuff is going to happen, but overall I'm a very happy customer," he said.
Amtrak says when something goes wrong -- it really goes wrong because there are only four tunnels with one track each to get into and out of Manhattan.
In a statement to Eyewitness News a spokesman for Amtrak said:
We apologize any time that we inconvenience any passenger. We want a system that works. We're working on making things better
The third rail was repaired by 1 p.m. and an investigation continues into what caused the incident.
Amtrak, LIRR and NJTransit share four tunnels under the East River, connecting Penn Station with points east and north, as well as the Sunnyside Yards where NJTransit keeps some trains at off-peak times.