In this Oct. 30, 2012 photo, water reaches the street level of the flooded Battery Park Underpass in New York.

(AP Photo/Louis Lanzano)

LONG BEACH, N.Y. -- New York transit officials marked a milestone in the aftermath of Superstorm Sandy on Wednesday by restoring limited service to the last of 10 branches of the Long Island Rail Road commuter line and declaring that nearly all New York City subway service was now operational. They also conceded work still needs to be done to alleviate overcrowding and slower than normal commutes since the Oct. 29 storm.

"Every day you'll see a little bit more and a little bit more of service coming back," said Joseph Lhota, CEO and chairman of the state's Metropolitan Transportation Authority, which operates commuter trains and the city's bus lines. "Slowly, but surely, the subway system has come back. We are currently at about 98 percent back to normal."

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Lhota joined LIRR President Helena Williams and state and local elected officials on a symbolic train ride to Long Beach on Wednesday morning, trumpeting train restoration to one of Long Island's hardest hit communities. The oceanfront city just outside New York suffered extensive damage to its picturesque boardwalk and thousands of homes were inundated by rising floodwaters.

The LIRR resumed a regular schedule on its nine other branches this week, although 19 trains were removed from the overall daily schedule because of limited access to four tunnels under the East River into Manhattan. The Long Beach branch, which is being operated by diesel trains because electrical service was still not available, was initially running only one train per hour.

Williams said the railroad was working with Amtrak, which owns the East River tunnels that were flooded in the storm, to restore the 19 canceled trains, but said it could be until January before full service is restored.

Because of fewer trains overall, each of which can carry as many as 2,000 commuters on average 10-car trains, commuters were contending with standing-room-only conditions during rush hours. In some instances, conductors have been unable to pass through the jammed cars to collect tickets.

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Johnny Grimmer, 22, who works in advertising sales, said he has had to contend with overcrowded trains since service was restored.

"I felt bad. I was squishing this girl into the door of the train, but that was only because this guy twice my size was squishing into me," he said in a telephone interview from his Manhattan office. "All of us would sway at the same time. There was nothing to grasp onto and people were falling into each other."

Grimmer conceded he had not been a fan of the railroad before the storm, but said conditions have gotten worse. "I think they could have done some better planning to deal with this storm," he said. "There is enough technology to plan for a storm like this."