In parts of Queens, some roads looked more like rivers. Firefighters helped push cars out of knee deep water on the Van Wyck on Jewel Avenue.
Fallen branches and even trees were also a problem. One fell in Ridgewood, closing down a road.
Nearly two inches of rain poured onto Central Park as the thunderstorms lumbered through, National Weather Service meteorologist John Cristantello said. They were "very slow-moving storms, so (the rain) is having time to accumulate," he said.
The Jones Beach Theater was evacuated in the midst of a show featuring rock bands R.E.M., Modest Mouse and the National, said George Gorman, deputy regional director for state parks. Officials tell fans to seek shelter whenever lightning threatens at the outdoor venue, he said.
One concertgoer was taken to a hospital with what appeared to be a minor injury; it wasn't clear how she had been hurt, Gorman said.
The amphitheater wasn't damaged, and the show resumed after about 90 minutes, he said.
Lightning temporarily disabled Nassau County's 911 system, but the problem was promptly fixed, police said. Residents who needed help were advised to call local police precincts in the meantime.
Meanwhile, downpours cut off service on a stretch of the subway system's F line in Queens. Parts of numerous streets and highways were closed because of flooding; in other places, cars sloshed through - or got stuck in - water up to their undercarriages.
Departing flights ran more than six hours late Saturday night at John F. Kennedy International Airport and more than three hours behind at Newark Liberty International Airport. Earlier, LaGuardia Airport also delays of as long as four hours.
Saturday night's game between the Texas Rangers and New York Mets was rained out and will be made up as part of a doubleheader Sunday with first game set to start at 1:10 p.m.