Best sit-down pie in NYC is Grimaldi's under the Brooklyn Bridge on the Brooklyn side.
Best on-the-go slice is La Famiglia near Times Square.
Best of the newer gourmet-style joints is Motorino's in the East Village.
Best Sicilian-style slice is Rosa's on Metropolitan Ave in Queens.
As for all the clowns on the thread saying that Chicago pizza is the best, well, I lived there for six years, and the Chicago version is delicious - but it isn't pizza. It's fried focaccia with pizza toppings. And the stuffed pizza is a scarcieddu - basically an enormous version of the Italian empanada.
And Uno's is the worst variety of Chicago pizza - that crud is glorified Pizza Hut at best. Giordano's is easily a hundred times better.