From the NYTs:
New York’s Last Natives
Q. What was the last organized American Indian tribe to occupy what are now the five boroughs? When did it leave?
A. You could make an argument for the Munsees. The purchase of Manhattan by Peter Minuit in 1626 was negotiated with the Munsee speakers of the Lenape (“the People”) of the Delaware Nation, according to information compiled by the National Museum of the American Indian. (Munsee is a dialect in the Algonquian language spoken by the Delaware.)
From 1630 to 1758, Munsees sold their lands piecemeal, first to the Dutch and then to the English, and the land that makes up the five modern boroughs “was essentially all sold by the beginning of the 18th century,” according to “Unearthing Gotham: The Archeology of New York City” (Yale University Press, 2001). A few Munsees lived on in the area. After the Seven Years’ War ended in 1763, they began heading west.
The Matinecocks inhabited northeastern Queens and Nassau County. Although they sold most of their land by 1800, many people in Queens claim Matinecock ancestry. A revival of the Matinecock Nation began 50 years ago on Long Island.
Over all, the Census Bureau estimated in 2006 that 23,000 American Indians and Alaskan natives lived in New York City. So in a genuine sense, American Indians are still here.
Turtle Talk 
As editor of DutchNewYork.com, concentrating on the 17th-century Dutch American colonies, I have to admit that my coverage of native American tribes is an area I’ve yet to explore. But it’s still new. The site will gain momentum as the 400th anniversary of Henry Hudson’s discovery of the Hudson River approaches, early next fall. I invite you and your readers to come visit, and even contribute, for full coverage of this topic.
Funny how people keep using that word — “discovery.”