Long Island Rail Road president Helena Williams said that service will be back to a near-normal schedule for Wednesday's morning peak hours.
She said most branches were in service for Tuesday's rush hour.
Trains are running on a holiday schedule.
Departures from Pennsylvania Station for Babylon are every half hour, with hourly departures for Ronkonkoma (ron-KONK'-uh-muh), Port Washington, Huntington and Long Beach. Trains are leaving for Hempstead and Oyster Bay every two hours.
The LIRR stopped all trains Sunday night amid a blizzard that brought a foot and a half of snow to New York City.
Limited service resumed on Tuesday, but many commuters were left standing at stations because of over-crowded trains.