The thunderstorms prompted brief tornado warnings and flash flood warnings before giving way to a sunny, humid day. Wind and heavy rain toppled trees onto cars and streets and left some shops shuttered and businesses struggling with shortages of workers.

There were delays of up to an hour and a half at John F. Kennedy International Airport and about an hour at LaGuardia International Airport due to the storms, said Alan Hicks, spokesman for the Port Authority of New York and New Jersey.

All subway lines in the city experienced delays or diversions, and some rail lines to Grand Central Terminal and some rail routes from New Jersey into Manhattan were shut down for more than an hour.

"We have been advising customers to avoid the system if possible because there is extensive flooding on the tracks," NYC Transit spokeswoman Marisa Baldel said.