Crews are continuing efforts around the clock to restore service on other branches.
However impacted ice above the 3rd rail and frozen switches remain a significant issue.
At Jamaica Station on the Long Island Rail Road, hundreds of people dozed in train cars frozen at the platform all day on Monday.
Others lay like refugees at the entrance to the train link to Kennedy and stood helpless at the ticket office, waiting in vain for good news to flash on the schedule screens.
Hours went by without a single train leaving with passengers.
Buses were knocked out, cabs were little more than a myth and those who tried walking out of the station were assailed with a hard, frigid wind that made snowflakes sting like needles.
"They tried, but they can't do much with this snow. It's just not stopping," said Sharray Jones, 20, headed home to Long Island after visiting friends.