check out this thread about a trip to NY I took a few months ago.http://www.pizzamaking.com/forum/index.php/topic,1616.0.html
Here is how I would rate the pizzerias based on my preferences
#1 Una Pizza Napoletanna, this is very similar to the pizza in Naples, but with a more sour dough, and much more olive oil on top of the pizza. Although it is my favorite place I have found in NY, you might not want to bother trying it because it is so similar to what you can find in Italy. They use a woodfired oven.
#2 Grimaldi's, In my opinion this is almost a perfectly even cross between a typical Neapolitan pizza, and a typical NY pizza. I have found this place to be very consistant. This pizzeria uses a coal fired oven, and has a really tasty crust. I have only tried the original location under the Brooklyn bridge, which is pretty easy to get to, and quite close to Manhattan.
#3 Patsy's original location. this is closer to a typical NY style pizza, but really thin. They do have the high heat advantage of a coal oven, but they can be inconsistent. I would suggest upgrading to "fresh" mozzarella. This pizzeria uses a coal fired oven.
#4 Lombardi's, this is supposedly the first pizzeria in America, and still one of the best. This pizzeria could easily tie with Patsy's for my third favorite. The pies are more consistently good, and the sauce is amazing. The crust is just slightly too bready for me (high gluten flour mixed too long), and since I am really a crust guy above all else Patsy's wins out. Lombardi's uses a coal oven.
Now, I have named my favorite "elite" NY pizzerias. As you are walking around the city, (especially in the Greenwich Village where you must go!) you will find a pizzeria on every major street. 99% of these places use normal gas fired ovens, and make the typical NY style pizza that we refer to as "street pizza" here on the forum. In general the quality of these places is high. I named some of the famous ones on the link above, but every time I go to NY I just wander into a place randomly and find the best NY street pizza of my trip. I suggest you try one that seems busy, and has fresh looking pies. Chances are you will not be disappointed. Also don't forget to try some garlic knots with a side of pizza sauce.
Also, I think NY has the best Chinese food and falafel sandwiches in the US, so you might want to try some while you are there.