NEW YORK - The nearly 400,000 New Yorkers who had been ordered to evacuate low-lying neighbourhoods because of Hurricane Irene were told they could go home Sunday afternoon, but officials said the city's transit system probably won't be up and running in time for the Monday morning commute.

That could mean a rough start to the work week for millions.

Overall, the city made it through the storm fairly well, Mayor Michael Bloomberg said in announcing he would lift the evacuation order covering 370,000 people by 3 p.m.

He said Irene inflicted significant damage, with retaining walls collapsing in some places and serious flooding across all the five boroughs.

But "whether we dodged a bullet or you look at it and said, 'God smiled on us,' the bottom line is, I'm happy to report, there do not seem to be any deaths attributable to the storm," the mayor said. He added: "All in all, we are in pretty good shape because of the extensive steps we took to prepare."

Among those steps was the shutting down of city subways, commuter rails and buses.

Jay Walder, chairman of the Metropolitan Transportation Authority, said it is not clear when service will be restored because damage to the various parts of the system will have to assessed first.

Walder said the shutdown -- the first time the nation's biggest transit system suspended all service because of a natural disaster -- was the right move, noting that some train yards were under water.

New York's subway system alone has more than 5 million riders a day.

"I think it's fair to say you're going to have a tough commute in the morning," Bloomberg said. "Tough commute tomorrow, but we have tough commutes all the time."

Around the city, firefighters rescued dozens of people from flooded homes on Staten Island, residents removed garbage and debris from clogged sewer gates, and eerily quiet roads became busy again soon after a weakened Irene came ashore at Brooklyn's Coney Island around 9 a.m. as a powerful tropical storm.

In Queens, bungalows floated down the street and emergency crews were checking to make sure no one was inside. There was heavy flooding in other parts of the city, but Manhattan was mostly spared.

Coney Island boardwalk landmarks like the red parachute drop tower, the Cyclone roller coaster, and Dino's Wonder Wheel appeared intact. Residents there pitched in to dislodge debris from the sewer gates.

"It's working," said Daniels Stevens, as a small whirlpool appeared where the water was draining out. "When we started, the water was almost up over the hubcaps on that parked car."

Irene weakened after landfall over the North Carolina coast Saturday, but it was still a huge storm with sustained winds of up to 65 mph as it hit the city. Coinciding with a tide that was higher than normal, water levels rose, but not as high as anticipated. They were quickly receding.

In Manhattan, some streets were flooded on the east and west side of the island, closing major thoroughfares such as the Henry Hudson Parkway and the FDR Drive. The Tappan Zee Bridge was closed because of flooding on the highway leading up to it.

Twelve-year-old Alex Cuglewski said he set his alarm for 3 a.m. so he could get up and watch Irene from his family's eight-floor oceanfront apartment in a stretch of Rockaway Beach where everyone was supposed to evacuate.

"It wasn't that bad. People evacuated for no reason," he said. Waves went up to the boardwalk but did not spill into his street.

Water from New York Harbor washed onto the sidewalk at Battery Park along the tip of the island. About a foot of water lapped over the wall of the marina in front of the New York Mercantile Exchange in lower Manhattan. A low-lying section of the promenade hugging Battery Park was also submerged, and much of the operational equipment for the ferries out to Staten and Ellis Island was damaged. It could take a day to get it up and running.

But the Sept. 11 Memorial and Museum sent a Twitter message that read: "None of the memorial trees were lost." About 400 trees have been planted ahead of the 10th anniversary next week. And the city's biggest utility said it was cautiously optimistic that it would not have to cut off power to Wall Street and 17,000 people.

Slowly cabs started appearing downtown and residents returned despite the evacuation order.

"It was a fun little adventure. I tried not to think about the hype and take things as they came," said Zander Lassen, 37, who spent the night at a boathouse watching sailboats.

Grace Tate, a Manhattan paralegal, found her herself stranded in the World Financial Center lobby with a front-row seat to the hurricane.

She had been determined to make it downtown for Sunday services at Trinity Church, only to learn they had been cancelled. Security and maintenance men who had spent the night in the building were her only company.

"First the earthquake and now this," she said as heavy rain pounded empty streets outside.

Bloomberg was right "to err on the side of overkill," Tate said of the mayor's insistent warnings to evacuate. "I think we need to be more respectful of nature."

Other neighbourhoods weren't as lucky. Coastal areas of Staten Island and parts of Queens had the most damage from flooding. Power was out to about 110,000 customers around the city and hundreds of thousands in Long Island.

All subway, bus and commuter rail service was suspended Saturday because of the danger of flooding and downed trees.