NY Pizza Suprema. It's on Eighth Avenue and 30th or thereabouts. The regular pie and the "upside down" pie (square with sauce on top of cheese) are standouts.
Hands down Lazzara's, on 38th b/t 7th and 8th. This is, IMO, not only the best in the area, but one of the top 5 in Manhattan. Also, you could try John's as well.