I've actually created a "pizza tour" one year over the summer and hit all of NYC's best. By borough...
Denino's on Pt Richmond Ave is the best by far, and then for dessert head across the street to "the original" Ralph's Ices.
DiFara's in Midwood is really homemade pizza...great. Not for tourists however as you will wait unless you hit it on a Tuesday at an off hour during the day...try the artichoke.
Tutonos on Coney Island is also very good. Nice this crust, great tangy sauce. Try a red and a white pie.
Grimaldis is my wife's favorite. We go once a year. As far as being crammed in, thats part of the experience. Y'all don't go Pats or Genos in Philly and expect white glove service do you? Get over yourselves. Thicker crust than Tutonos and Difara's, and comparable to Lombardi's.
MY 5 STAR RECOMMENDATION*****
L&B Spumoni Gardens on 86th St in bensonhurst...the best pie ever made is their square. In the summer its beautiful to sit out on their "patio" and just pig out. Wonderfully thick and tangy. Sauce on tyop of the cheese. Then get yourself a rainbow spumoni to wash it down. Their restaurant food isn't bad either.
Peppinos in Bay Ridge on 3rd Ave is also very good, much like Grimaldi's and Lombardis...then head down the block to Amonia for some great Greek Desserts. Also has wonderful cheesesteaks.
John's on bleeker is good pizzeria style pizza. Great toppings (no not pineapple and that crap, but real pizza toppings.
Lombardi's on Spring is also very good, and founded by relatives of mine way back when. My uncles wouldn't be disappointed with what its turned out to be.
Nicks is good, but overrated. Certainly not worth the trek. Would compare it to Peppinos, but Peppinos is a few blocks from me. Don't get me wrong, its good pizza, but there are better out there in the city.
Never been to a pizza place in the Bronx, so I can't comment of their places.
So perhaps I'm biased, but i think Brooklyn can claim to be the home of the best pizza in NYC, and therefore, the world!