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.)
Turtle Talk 