More than a dozen people had to be rescued from one flooded part of the highway in the Bronx.
Commuters had to wade through waist-deep waters in parts of the city such as in Upper Manhattan.
The interim president of New York City Transit, Sarah Feinberg said on Twitter: “Drains are working remarkably well, and NYCT crews are, as always, working hard and fast and doing great work.
“Give them room to work and be safe. Water is receding. Stay alert for additional storms.