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For pizza-by-the-slice, my favorite place in Manhattan is Pizza Suprema, on 8th Avenue between 30th and 31st streets (near Penn Station and the General Post Office). For whole pies, John's on Bleecker Street (in Greenwich Village), and Nick's on 2nd Avenue and 94th Street are both very good.
Some of the trendy, new pizzerias, like Co. and Motorino, get very good reviews from the food critics and from some FT regulars, but I have not tried either one of those.