This thread is long over due.
For me, it's a toss up between the really good pies at New Jersey Pizza on Cedar just west of 4th, and Ni Marcos on Beaver south of the tracks. New Jersey Pizza is slow (420 friendly), and every time I have ordered, I show up late and still wait for my pizza. But, they are really good and use local fresh ingredients for their toppings. Their green chili pizza is the best I ever had. I only had their's and one other.
Ni Marco's is good, too, and they are reliable and get their times right.
I know Jake's old place was good, but they shut down. Alpine is ketchup on a cracker, and the City Pizza is Dominos in a different wrapper.
Nothing more enjoyable than a good hike out of town.