Even with pizza, you get what you pay for. Without a doubt, Una Pizza Napoletana's Anthony Mangieri makes the best pizza in New York City. He uses the best possible ingredients (including imported wood for his oven), and hand makes each and every pizza. The experience itself is also amazing, since from the tables one gets to watch Anthony make each pizza.
It's expensive - two individual pizzas and wine will run you over $60 - though when did a filling spectacular dinner in Manhattan cost less than that? Una Pizza is certainly worth a trip.