The squat clapboard house overlooking the Hudson River in the West Village might not seem like an obvious place for a Native American prayer center.
Its graffiti-strewn facade faces the busy West Side Highway, with a city bus stop out front. It once housed a series of bars, and the back of the building faces tiny Weehawken Street, which has traditionally been a popular gathering spot for gay and transgender people.
The house’s ground floor now sits directly on Manhattan soil, said Jean-Louis Goldwater Bourgeois, 76, a wealthy activist who bought the property in 2006. He says he is essentially donating it back to its original owners: the Lenape Indians.
Mr. Bourgeois wants the building to be a prayer house, to be owned and operated by the Lenape nation, which inhabited Manhattan before it was appropriated by European settlers.
Mr. Bourgeois pointed to a hole recently jackhammered through the thick concrete flooring of the …