Lucali is pretty magical, but I can't get over the raw basil. I really don't know why people find that preferable to cooked basil. Otherwise, I'd crown it the best.
Guisepinna's in Park Slope mimics Lucali in many ways with the pizza-making in the dining room, and I think it's nearly as good without an hour wait.
Lombardi's is good for heavily topped pizza, but their margherita is mediocre, and it's a pretty shitty dining experience by most objective measures. Getting seated by a host wearing a headset is just sinful, as is the abundance of middle-brow decor.
John's is really good, but my experience is limited.
Artichoke Basille's is outstanding, under the condition that abject gluttony and 2,000 calorie slices of pizza don't turn you off. Otherwise, the guilt will just drown out the taste. I've heard some quality complaints recently though.
Roberta's in Bushwick is totally worthy of its reputation. It's a really great dining experience and worth the trip to the Wild West of Hipsterdom. The night I went they weren't offering their signature pizza (bee sting) but we had two others and both were nearly perfect.
I've had a couple of my best pizzas at Speedy Romeo and Nice Pizza in Clinton Hill and Bed-Stuy respectively, but they're probably too new to warrant much pull for this sort of distinction.
As for slices, my favorite slices in NYC might be in the Lower East Side at Nonna's, which specializes in the grandma slice, or at Three Luigi's in Clinton Hill, which does a perfect greasy pepperoni slice.
I can't say about the other big names (Grimaldi's, Juliana's, Di Fara, Totonno's, L&B Spumoni Gardens, etc.) Based on photos alone, Juliana's looks superior to Grimaldi's in DUMBO, and Di Fara seems like it's the superior of old-school pizzeria's in South Brooklyn.
The troubling thing is that there's really so much competition for high end pizza that you could probably find twenty other pizzerias that on any given night could give you the best pizza you'd ever had. Every week it seems like there's a new one, and it makes forming an opinion of greatest pizza an almost entirely sentimental or "experience" related task. The degree of refinement in the pizza market really makes objective analysis futile, and even if you tried to name the best, the margin of error that every pizza is prone to could leave you with a relatively mediocre pizza on any particular visit.