Limited service resumed at 5:40 a.m. Monday, and Metropolitan Transportation Authority spokesman Charles Seaton said subways were running smoothly, if a little more slowly than usual. He said commuters could expect a bit more crowding but otherwise service was normal.
Riders who expected a difficult commute said they were relieved.
"The subway is running very well. I can't believe it, they did a great job," said Dominic Cecala, who took an E train from the city's west side to lower Manhattan. "If they hadn't stopped the trains on Saturday, it would have been a mess."
The MTA's decision to halt all subways, buses and commuter trains in preparation for the storm - the first time a natural disaster ever closed the system down - had threatened to disrupt the start of the work week in the nation's most populous metropolitan area.
Ferries to and from Staten Island were running well. Joe Dinguis, a 56-year old career counselor, expected problems getting from his home in Staten Island to his job in Brooklyn. But as he disembarked from the ferry in lower Manhattan, he said his trip had gone smoothly so far.
"Everything's fine today," including the Staten Island Railway, he said.
The center of Irene passed over Central Park at midmorning Sunday packing 65 mph winds, but damage to New York City was less than feared. An evacuation order for low-lying city neighborhoods was lifted Sunday afternoon. By Sunday night, limited bus service started up.
With a daily ridership of more than 5 million, New York City's subway system is by far the nation's largest. Many New Yorkers do not have cars and would be hard-pressed to get around without the subway.
The MTA had done simulated runs throughout the subway system in order to be ready for Monday's commute.
"Suspending service allowed the MTA to secure equipment, thus expediting the return to service," New York Gov. Andrew Cuomo said in a statement.
For updates please visit: http://www.mta.info