Grimaldis (in Brooklyn), Totonnos, or any number of good Brick Oven places if that's your thing.
For regular-style, Joe's on Bleecker in the West Village, and Pizza Suprema by Penn Station. IMO, Ray's has gone way downhill.
While you're in NYC, get a great burger at Corner Bistro in the West Village or JG Melon around 74th Street on the UES.