"We are on the scene and the whale has passed," Robert DiGiovanni, director of the Riverhead Foundation for Marine Research and Preservation, said.
The finback whale, the second biggest animal species in the world after the blue whale, was found ashore early on Wednesday in the Breezy Point neighborhood of Queens.
Police and firefighters began carefully spraying it with water to keep it alive until experts could take over.
Mendy Garron, a specialist from the National Marine Fisheries Service, told AFP on Wednesday that the outlook was not promising, describing the whale as "really emaciated."
After a post-mortem examination, the next big challenge will be the "disposal of the carcass," Gerron said on Thursday.
"You need a lot of heavy equipment... they are working on it right now," she said. "They are looking at... either a potential site to bury it or a landfill that can take the soft tissue."
Adult finbacks, which can reach up to 27 meters (88 feet) and weigh up to 70 tons, are found in all the world's oceans and can live up to 100 years.
According to the Riverhead Foundation, which is based on Long Island, at least 25 species of whales and dolphins have been seen in the New York region.