Most of the really great pizzerias are in Brooklyn, Queens, and Staten Island.
However, John's of Bleecker Street is located in lower Manhattan. They specialize in a heavenly thin crust pizza.http://www.johnsofbleeckerstreet.com/directions.html
Also, Ray's Pizza is located at the corner of 9th Street and 6th Avenue. There ore other "Famous Ray's" all over NY - this is the only "real" one. This is probably the place that started my love affair with the pizza slice. Theirs is loaded with cheese. I'd also suggest their Sicilian slice - it's something I always come back for whenever I'm back in NYC.