NEW YORK

Commuters streaming into New York City this morning endured long waits and crowded trains, giving the recovering transit system a stress test a week after Superstorm Sandy ravaged the Northeast.

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 waterlogged tunnels still weren’t ready for Monday’s rush hour and that fewerthan 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.