I moved out of Rochester 5 years ago but:
Nino's foccaccia/sicilian style were very good and I hear they still are
Chester Cab chicago stuffed was great but i hear they may have gone down hill
Pizza Stop - by far the best NYC style slices in the city. The owner has been politically outspoken and I think that has clouded people's opinions.
Brooklyn Joes - solid slice shop, related owners to Pizza Stop if I recall correctly
Fiamma is good Neapolitan
Pizza Wizard looks phenomenal. Detroit style pies. I have not tried it.
Every Pontillo's is different. Some are radically different than others. Bushnell's Basin was the best Pontillo's I have had.
Columbini's was great when we lived on the west side. Haven't tried it in years.