Once upon a time it was true that Sally's had the best, going solely by quality of pizza and not counting service, hassle, atmosphere, etc. The good news is that it is rarely a hassle any more because there is rarely a line these days. The bad news is that there is a reason: the quality and cleanliness have plummeted. I don't even consider it an option any more, nor does anyone I know--including people who were loyalists for decades.
The original Pepe's is still great, especially for the white clam pie. No one comes close on that one. And all the others are still solid.
BAR is also as great as it ever was. It gets a boost for interesting toppings (mashed potato, bacon, red pie being my favorite). But you gotta eat it fast and fresh, because the crust is so thin that it doesn't hold up well over time. And I'm talking like 15 minutes.
Modern is still the place where most people who live and/or work in New Haven go for their New Haven style pizza. Take out is always 20 minutes, they have more varied toppings than Pepe's or Sally's (eggplant, artichoke hearts, red pie being my favorite), and in my experience they are very consistent except that the pies can be underdone and/or soggy sometimes. I have solved this by ordering "light cheese, well done." This results in a perfect pie for my tastes.
I second Roseland in Derby as a worthy entry.
Fishy, I don't know where you are in Westchester, but I had some great pizza at Coal's in Port Chester before a show at the Capitol Theatre, and I definitely plan to return there when I go back to the Capitol. A very impressive beer list, too, as well as some very unique grilled chicken wings.