For my money, the best pizza in the city. While I haven't tried Totonno's, I would rate John's above the other famed NYC pizzerias....Lombardi's, Patsy's and Grimaldi's. All of those serve some fine pizza, and are definitely far better than your average slice joint, but John's is just a notch better. Plus, its got a great Bleecker St. location in the heart of the Village.
There's probably a better version of this somewhere, but here's a decent little summary of the history of pizza in NY that includes pizza family tree that connects Lombardi's, Patsy's and Grimaldi's. It even gives you the scoop behind all of the Ray's Pizza joints in the city.
New York Pizza, Part INew York Pizza, Part II