The best pizza is, by definition, pizza made in New York.
You just can't compare Chicago and New York-style pizzas. In this contest everyone's a winner. They're too different to pit one against another, and everyone has their own die-hard opinion. Wars have been started over less.If by New York, you mean, Chicago, than yes.
We've had New Yawkers poo-poo our gobs of cheese, square slices and hidden toppings at Pequods. (btw Chicago thin is still very, very good. Eat at "Piece")
Likewise, we criticize NY's lack of cheese, general flatness and even the style of eating (it's not a Fruit Roll-up btw). To each his own, and never the twain shall meet. If you're looking for a easy to eat, fold over pizza eat it in a New York second then New York's your place.
New York could be better whether NYC deserves it or not "just because it's New Yak"....
New York rarely loses at anything strictly because it seems that everybody know things about New York more than Chicago. Just based on sheer exposure through media, movies, tv, etc. and because most critics of Chicago pizza A) had their taste buds dulled by decades of Domino's crap or B) they're atheist pinko commies that hate puppies, children, and love.