NEW YORK » Commuters streaming into New York City today endured long waits and crowded trains, giving the recovering transit system a stress test a week after Superstorm Sandy ravaged the eastern third of the country, with New York and New Jersey bearing the brunt of the destruction.

Trains were so crowded today on the Long Island Rail Road that dozens of people missed their trains. With PATH trains between New Jersey and Manhattan still out, lines for the ferry in Jersey City quickly stretched to several hundred people by daybreak.

One commuter in line pleaded into his cellphone, “Can I please work from home? This is outrageous,” but many more took the complicated commute as just another challenge after a difficult week.

“There’s not much we can do. We’ll get there whatever time we can, and our jobs have to understand. It’s better late than absent,” said Louis Holmes of Bayonne, as he waited to board a ferry in Jersey City to his job as a security guard at Manhattan’s Sept. 11 memorial site.

The good news in New York City was that, unlike last week, service on key subway lines connecting Manhattan and Brooklyn under the East River had been restored. But officials warned that other water-logged tunnels still weren’t ready for today’s rush hour and that fewer-than-normal trains were running — a recipe for a difficult commute.

On Long Island, Janice Gholson could not get off her train from Ronkonkoma and Wyandanch because of overcrowding, and ended up overshooting her stop.

“I’ve never taken the train before. There were people blocking the doorway so I got stuck on the train,” she said.

Mayor Michael Bloomberg took the subway to work today. He was joined by many of the students returning to class in the nation’s largest school system. About 90 percent of the 1,700 schools reopened for the first time since Sandy hit last Monday, the mayor said.

At Public School 2 in Chinatown, the playground was once again full of the sounds of children laughing and shouting as they played basketball before school started. Samantha Martin, a fifth-grader at P.S. 75 on the Upper West Side, made it to school from the Bronx with time to spare on the subway.

“It was packed but I’m happy. Home is boring!” Martin said.

The longer commute times were actually a lesser problem for many families who left homes and apartments that have been without power for almost a week. In Westchester County, Liliana Matos said dropping her boys off at Colonial School in Pelham gave her a chance to “call Con Ed and get on their backs” about the loss of power. For the last three days, they have been staying at a hotel because the house is too cold.

In Jersey City, investment advisor Barbara Colucci, was traveling from a house without power and the family’s car was low on fuel because of persistent gasoline shortages.

“I can’t wait until the PATH and light rail are up and running again, but first I’d like power in my house quite honestly,” she said. “We’re sleeping on air mattresses but we have heat so we can’t complain but I’d like to get back to a bed — it’s been awhile — and back to a regular commute.”

Repair crews have been laboring around-the-clock in response to the worst natural disaster in the transit system’s 108-year history, Metropolitan Transportation Authority Chairman Joseph Lhota said Sunday.

“We are in uncharted territory with bringing this system back because of the amount of damage and saltwater in our system,” Lhota said. “It’s an old system … and it’s just had a major accident.”

World Trade Center steam fitter Scott Sire got to Manhattan on time, at 6:05 a.m. off a regular Academy bus that took him from home in Hazlet, N.J. in 40 minutes. He normally takes a PATH train, but it’s not running.

“Every day gets a little bit better,” said the 49-year-old worker. “But we had a setback last night; we lost power, again, after a transformer blew — and the Cowboys lost, just after our lights went out!”

The MTA planned to take the unusual step of using flatbed trucks to deliver 20 subway cars to the hard-hit Far Rockaway section of Queens and set up a temporary shuttle line.

Though New York and New Jersey bore the brunt of Sandy’s destruction, at its peak, the storm reached 1,000 miles across, killed more than 100 people in 10 states, knocked out power to 8.5 million homes and businesses and canceled nearly 20,000 flights. Damage has been estimated $50 billion, making Sandy the second most expensive storm in U.S. history, behind Hurricane Katrina.

The superstorm also created a fuel shortage that has forced New Jersey to enforce odd-even rationing for motorists. But there was no rationing in New York City, where the search for gas became a maddening scavenger hunt over the weekend.

Sire said he felt lucky to fill his car tank, but he added: “We’re a gallon away from turning into a Third World country.”

The coming week could bring other challenges — namely an Election Day without power in polling places, and a nor’easter expected hit the area by Wednesday, with the potential for 55 mph gusts and more beach erosion, flooding and rain.

In New York, power has been restored to nearly 80 percent of its customers who were blacked out in the storm, but efforts to get everyone back on line could be hampered by more wet, windy weather. But crews were making some progress.

On the Upper West Side, 17-year-old Anna Riley-Shepard waited for her yellow school bus to take her to a private school in the Bronx. Her school has been without power for a week. It came back yesterday, they were told.

“You don’t really realize how important a routine is until you’re out of one,” she said.

Associated Press writers Jennifer Peltz, Leanne Italie, Michael Hill, Karen Matthews, Larry Neumeister and Verena Dobnik contributed to this report in New York City. Contributions from Samantha Henry in Jersey City, Frank Eltman on Long Island and Jim Fitzgerald in Westchester County.