The National Weather Service just issued an "URBAN FLOOD ADVISORY" for NYC (except Staten Island) until 11:30 a.m., noting that thunderstorms in the area may produce 1.5 inches of rain/hour and will cause street and highway flooding. And maybe subway flooding? Yikes.
Update: While the storm seems to be over, there's a bit of flooding in certain areas, namely the FDR Drive. Some vehicles are disabled due to a foot of water on the road!