Sunday's rain is the most recorded in New York City in a single day since the National Weather Service started keeping records 116 years ago, the New York Daily News reported.
Forecasters said more rain was expected Monday and issued a flash-flood warning.
"This is what you would expect in a major hurricane," said Steve Wistar, senior meteorologist at AccuWeather.
Nearly 8 inches of rain had fallen at Kennedy International Airport by 9 p.m. Sunday.
Central Park, where the city's official rainfall total is recorded, received 5.8 inches by 10:45 p.m., making it the fifth-wettest day of all time there, the News said.
The rain resulted in scattered power outages and fender-benders and some cars were caught in roadway flooding. Water also flooded some subway tunnels, knocking out parts of seven train routes.
The New York Post said flooding nearly killed two Staten Island construction workers. The two had taken an elevator to the basement of the Staten Island Hotel, which is being converted into senior living residences.
When they reached the basement, which was flooded, water rushed into the elevator car, destroying its electronics
"We thought we were dead," Ed Tyler, 26, one of the rescued construction workers told the New York Daily News. "I literally thought I was going to die."
The two were able to call 911 for help. When fire department officials arrived, the elevator shaft was filling with water.
"They were happy to see us," Capt. James Melvin of Ladder Co. 86 told the Post. "They were in there for about an hour, and they didn't know what was going to happen."