Officials in that city had every road closed because of downed trees, power lines and debris.
There were almost 50 reports of hail in states including Ohio, Pennsylvania, New York, and CT, the National Weather Service (NWS) said.
Rainfall totals likely will be the highest in the mid-Atlantic, where more than 4 inches is possible in certain spots.
Almost 500,000 customers in New York, New Jersey, Connecticut, Pennsylvania, and Virginia were without power by late Tuesday night, fewer power outages than earlier Tuesday, tracking service PowerOutage.us said.
Much of the East will see rain in the next three days. Police in Newburg said the girl and her mother had arrived home and were unloading the auto when strong winds knocked the tree onto the vehicle. A 3-year-old child in the auto was not harmed, according to the Connecticut State Police.
The powerful thunderstorms that swept through the northeast Tuesday afternoon left a man and 11-year-old girl dead.
In New Fairfield, officials said a 41-year-old woman was killed when a tree fell on her vehicle.
Cell phone video showed Tuesday's risky winds bending and breaking trees in Danbury. In Maryland, a commuter train was stranded in several feet of water, forcing people to move to the top level of the train vehicle.
Golf-ball sized hail pounded Saugerties, New York. He deployed members of the New York National Guard to assist with recovery operations.
New York Gov. Andrew Cuomo declared a state of emergency in Putnam, Dutchess, Orange and Sullivan counties.