With storm flooding shutting down parts of New York's subway, trees blocking roads and gas shortages across the region, some of New York's commuters find the ferry is their best way to get to work.

The destruction wrought by Sandy, which crashed into New York on Monday night, has left much of the region's transportation system damaged, and almost severed the boroughs of Queens and Brooklyn from Manhattan.

For residents of the two areas, their best and in some cases only hope lies in the East River ferry, which reopened mid-week.

Brooklyn Heights resident Gavin Manly had kept a close eye out for any news that the ferry service would be up and running again.

"On Facebook, I saw that at 6:00 am, something like that," he told AFP, as he waited in line for the ferry.

"I walked to the boat from Brooklyn Heights, which is like six miles, or something like that."

After a 10-minute, $4-ride, he arrived on Manhattan and headed for his office at 10th and 37th street.

Without the ferry, he said, "we wouldn't be in the city... today."

Casey McDevitt, who works for Facebook in Manhattan, needed to get to a midday meeting in Midtown.

He had hoped to drive a car into the city, but then she heard that Mayor Michael Bloomberg had issued an order barring vehicles carrying less than three passengers from entering Manhattan.

"I tried looking around, I put up a note in my building, but people were not coming in."

The ferry, he said, was now "the only option you can get unless you can get multiple people to share a cab with."

Under normal circumstances, New York Waterway's East River Ferry serves 10 stations along the East River. But with the subway outage and car restrictions rendering it a virtual lifeline, a simplified route has been put in place.

For now, it is running on a northern and southern loop, each with just three stops, the former operating every 15 minutes and the latter every 30 minutes.

With its ticketing equipment damaged in the storm, the ferry operator was forced to sell tickets onboard the ship, and for purchase with cash only.

On Thursday evening, around 2,000 people lined up on 34th Street in a queue stretching hundreds of meters, a police officer said, in a desperate bid to board the ferry and get to their homes.

"I have never had to deal with anything like this. It's been pretty insane," said Chris Radditz, an East River Ferry employee working to organize would-be passengers into orderly lines.

"People are very frustrated," he acknowledged, saying the company was letting the maximum permitted number of passengers -- 144 and no more -- on each boat.

Police officers were stationed alongside the chaotic lines to keep things under control and reason with the crowd.

"Everyone past that point, you're not going to make it!" one officer warned would-be passengers as night fell on Thursday.

"Don't wait here, you're gonna waste your time!" he said to a collective groan.

Sarah Golden had lined up early to make sure she made the cut.

"They made sure to tell me that the last boat was at six... they put the fear into me," she said.

But others weren't as prepared.

"Why are you stopping so early," one angry older man asked. "Are there any kayaks or what?"

Others were more understanding, pointing out that Sandy created unprecedented difficulties for the city and its transport system.

"What can you do? There was a hurricane that happened, there's not a whole lot to expect," one man said.