Earlier, tornado warnings had been issued for Dutchess, Orange, Sullivan and Ulster counties in New York and Fairfield County in Connecticut with at least one tornado reported in Eldred, Sullivan County.
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The storms brought damaging wind, heavy rain, and hail, especially north and west of the city where they were the strongest. Hurricane-force winds of 65 to 78 mph were reported in the Hudson Valley.
The storms toppled trees and power lines across the area including in Mahwah New Jersey, where a tree crushed a garage. The homeowner, Al Vallese, said a show car worth at least $100,000 was destroyed.
An 11-year-old girl was seriously injured when a tree fell onto a car in Newburgh. She was trapped inside the car and had to be extricated. She was listed in very serious condition.
Metro North service in and out of Grand Central Terminal was temporarily suspended due to the severe weather, and the terminal was jammed with thousands of commuters at the height of rush hour. Officials say there were multiple downed trees on the lines.
Hudson Line service has since resumed with delays between Grand Central and Croton-Harmon. Service remains suspended north of Croton-Harmon.
Harlem Line service has resumed with limited service between Grand Central and White Plains and very limited service between White Plains and Mount Kisco. Service north of Mount Kisco remains suspended due to the downed trees.
Amtrak suspended service between New York City and New Haven.
New Jersey Transit service in and out of Hoboken Terminal Station was subject to 60 minute delays in both directions due to debris on the tracks.
The Port Authority Bus Terminal also reported delays, and drivers faced problems on the roads due to flooding and fallen trees.
The three major airports serving the city were all experiencing flight delays of an hour or more.
Here's a look at the severe thunderstorm as it plowed through Saugerties, New York.
This line of storms was expected to clear eastern Long Island and the Jersey Shore later in the evening, but there still could be showers and a rumble of thunder into the night.
Keep an eye to the sky and take shelter when you hear that first rumble of thunder. Remember, if you can hear the thunder, you're close enough to be struck by lightning.
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