John's is one of my old favorites. Located on Bleecker Street near 7th Avenue, the quality has slipped a bit over the years, but it still qualifies as a top-notch NY pizza place. There are no slices.
Ray's, on the other hand, is all about slices, although you can get a pie here, too. Many places claim to be the original Rays, but the first and best one is on the corner of West 11th Street and 6th Avenue. It's heaven on Earth and probably the best pizza in the world.