• Amtrak ran trains Thursday between Boston and New Haven, Conn., and from Newark, N.J., to Washington and other points south. By midday, water from one of two flooded tunnels under the Hudson River had been pumped out. The first train into New York City was expected at 8:45 p.m. Thursday. There was no estimate on when service to the north would resume.

• Commuter trains from the north and east of New York City also crept back to life but on limited schedules.

• Most of New Jersey’s mass transit systems remained shut.

• Those who couldn’t take mass transit were stuck on clogged highways and in long lines at gas stations.

• Cruise terminals in Manhattan and Brooklyn remain closed. Several ships diverted to Boston, including at least one that rode out the storm at sea. Passengers aboard the Norwegian Gem reported 40- to 50-foot waves rocking the ship and people vomiting in the hallways.

Those trying to travel within New York City faced major challenges.

Police peered into the window of every car trying to enter Manhattan to ensure that drivers where following emergency carpool rules. It there weren’t at least three people in the car, they were ordered off bridges and highways. Once on the island, they faced massive gridlock.

The subway – which handles 5.3 million passengers on a typical workday – wasn’t running south of midtown or out to Brooklyn. They left many commuters waiting for the few seats on temporary shuttle buses into Manhattan.

At one Brooklyn bus stop, more than 1,000 people snaked through police barricades. At another pickup point, passengers rushed the door when a bus pulled up. It filled instantly, leaving most people stranded at the curb.

Others dusted off their bikes or just prepared for a lengthy walk.

Those able to take the subway were thankful.

Technology worker Ronnie Abraham was trying to get from Penn Station to Harlem on the subway – a 20-minute trip. Buses fighting worse-than-usual traffic were taking 2 1/2 hours to make the same journey.

“It’s the lifeline of the city,” Abraham said of the subway.

Koenig reported from Dallas. Contributing to this report were Associated Press writers Verena Dobnik, Meghan Barr and Adam Geller in New York and Joan Lowy in Washington.