I was on a neighborhood tour of the Lower West Side a few weeks back and this came up when we sampled slices from what I think was the 2nd oldest pizzeria in NY. The guides attributed it to two things. One, the water used, the NY water supply comes from springs in the Catskills Mountains which have some sort of environmental protections. The other is the quality of the ingredients, the guide pointed out that the simple slice of cheese pizza didn't have any oil pooling on top of the cheese, cheap cheese will result in the oil separating during the cooking processed (that seems legit based on the pizza I get in TX).
I've been to small towns with a "House of Pizza" that made an awful flavorless and bready crust, and the locals loved it because they had no reference for anything better.
Recently I started making my own with a recipe similar to what was posted here (but mostly from Ken Forkish's book The Elements of Pizza), and I'm pretty happy with the results so far. It's at least something to hold me over until trips home.