The flooding led to the suspension of international flight arrivals at the airport on Sunday and the passengers at Terminal 4 have been diverted to other terminals, said the Port Authority of New York and New Jersey.
The water leaked from the ceiling onto a check-in counter covering large areas of the floor, local media reported.
Local media quoted a spokesperson of the Port Authority as saying that "about 3 inches of water was inside the west end of Terminal 4".
The suspension of flights further added to the misery of people stranded at the airport, after a powerful winter storm last week led to the cancellation and delay of hundreds of flights.
Massive delays, walls of people in terminals, complaints of hours-long waits to get to a gate after landing, then hours more to get checked baggage were some of the cries of the stranded passengers, who took to the social media, to vent out their anger.
Many were reported to be waiting for hours at the baggage claim after getting off the plane on Saturday.
Two Air India's Delhi to New York flights had been delayed indefinitely on Sunday, as permission to fly into the airport was not available due to inclement weather.
The airport website says that Terminal 4 is the major gateway for international arrivals at JFK airport.(ANI)