Breezy Point, Queens, was hit with winds as high as 85 mph at 10:58 a.m. and the Canarsie section of Brooklyn was hit with winds as high as 110 mph seven minutes later, said National Weather Service meteorologist Joey Picca.
A tornado watch means conditions are favorable for isolated tornadoes.
Meteorologists from the weather service, which confirmed the tornado strikes, surveyed the two weather-damaged areas in New York City on Saturday afternoon.
Firefighters were called to the waterfront community of Breezy Point just before 11:20 a.m., where a tornado touched down, shattering glass, peeling roofs off beach cabanas and sending plastic kayaks twirling into the air.
"It was a big black funnel," said Gregory Fillinger, 50, a 20-year resident of Breezy Point, the western end of the Rockaway peninsula.
Matt Schaffer, 18, a maintenance worker at the Surf Club, a private beach club badly damaged in the event, said "it sounded like a freight train."
"I saw the Dumpsters picked up and go across parking lot," Schaffer said.
There were no injuries, but there was structural damage and sporadic power outages, New York City Office of Emergency Management spokesman Christopher Miller said.
A tornado warning for Queens and Brooklyn was issued at 10:40 a.m. through the National Weather Service's CMass system, Miller said, which sends texts to cellphones.
At noon, firefighters responded to a second tornado on Canarsie Road near the Belt Parkway in Brooklyn. Radar data, video and witness reports confirmed that the cyclone that hit New York City was a tornado, National Weather Service meteorologist Dan Hofmann said.
An eastbound storm system is expected to bring heavy rain, hail, strong winds to the metropolitan area throughout Saturday, forecasters said.
"We'll be keeping an eye on this over the next few hours," said Stark. "Things could change very rapidly into the evening."
"The main threat now is damaging wind gusts," Stark said.
The storm could pack winds as fast at 58 mph and bring quarter-sized hail, Stark said, if it doesn't weaken as it moves east toward the Island.
Flight delays are expected at area airports including John F. Kennedy, LaGuardia and Newark. The Federal Aviation Administration recommends travelers check with their airlines.
There were no official warnings for Long Island by noon Saturday. As a precaution, residents should secure any outdoor furniture and have a plan to get to a basement or low-lying area, Stark said.
Nassau County activated its Emergency Operations Center at the Morrelly Homeland Security Center in Bethpage at 11 a.m. on Saturday, officials said. County and state agencies were to meet at the center beginning at 5 p.m. Saturday, said John Bruckbauer, deputy commissioner at the Office of Emergency Management.
The county has requested officials from the State Police Department, New York State Office of Emergency Management, State Department of Transportation and LIPA, as well as the county police, fire departments, Department of Public Works and representatives the county's townships, said Brian Nevin, spokesman to Nassau County Executive Edward Mangano.
"There is currently nothing imminent for the area, but additional storms are likely to fire in an unstable air mass as we go through the afternoon," Bruckbauer told his staff in an afternoon email. "These storms will have the potential to be severe with damaging winds, hail, heavy downpours, and even a tornado threat. The other concern would be when a line of storms, now developing in east-central PA, reaches the area. This would bring the potential for damaging wind gusts as high as 50-75 mph in the vicinity of 6-8 p.m. this evening."
In September 2010, tornadoes touched down in Brooklyn and central Queens, killing a Pennsylvania woman on the Grand Central Parkway.
"It's not every year, but I'm not going to say it's uncommon because we are going through a season change right now," Stark said.
Drier, mild weather with temperatures in the 70s is expected after the storm Sunday and Monday.
"It will definitely feel more fall like after this," Stark said.
With Robert Brodsky and Matthew Chayes