Five of the 16 people confirmed dead across the US and Canada killed by Storm Sandy lost their lives in New York.
Streets in the city filled with water, worrying some that the closed subway system would be deluged. At least seven stations have been covered in water.
US President Barack Obama has declared a major disaster in New York and Long Island.
A surge of nearly four metres in the sea coupled with high tides from a full moon caused record levels of water in Manhattan, southern Brooklyn and southern Queens.
Utility workers trapped by rising water inside a power station in lower Manhattan had to be rescued with inflatable boats.
Flooding even caused high alert at a New Jersey nuclear power plant.
“You would never think this would happen in New York, so the best we could do now is not to panic. The NYPD (New York Police Department) is doing all they can. They have a lot of patrol cars going to every single block. People just have to stay civil,” said stranded in Manhattan resident Rohit Massy.
During the night, more than 200 patients, including 20 infants from the neonatal intensive care unit, had to be evacuated from a New York University hospital due to a power cut and the failure of a back-up generator.
The largest storm to hit mainland America brought fire as well as water. At least 25 people had to be rescued from a series of blazes at apartment blocks in Queens. Strong winds spread the flames and prevented fire engines getting close.
Millions of people are without power, and authorities say the lights could stay off for more than a week.