The absolute best pizza I've had here was actually in Weehawken, NJ. It was a small dive that had an actual brick oven.
There is a place on Greenwich Ave. in Greenwich, CT called the Pizza Factory. They actually sold out and aren't quite as good as they were a couple of years ago. There pizza was really good.
None of these are NYC though.
As for NYC, they all serve New York style pizza and are all pretty much made the same exact way, you can practically go anywhere and get it and it will pretty much taste the same. It's good, but my favorite is thin crust (the crackery crust), but that is really hard to find here.
For NY style pizza, there are only really three things that could make one differ form the other. The oven it's cooked in, the dough it's made with and the tomato sauce. Very few of them don't use prepackaged ingredients. Those that don't will probably have better pizza. They are just far and few between.