Philomena's is the real deal, but the square slice is the reason to go there. It's not a traditional Sicilian, but more of a Romana style that uses super wet dough that he bakes directly on the stone. It's so crispy, yet airy & light. Very underrated spot.
Joe & Pat's is very good. It's like a much thinner version of Grimaldi's. I could finish an entire large pie & probably eat half of a second one. If you go with people, keep this in mind.
Sally's is my favorite of the New Haven spots, but Portnoy managed to move these places into legendary status when in reality every single one of them are a notch below the best NYC pizzerias. New Haven pizza by definition has good char on the bottom, but they're all missing something I can't quite put my finger on. Maybe it's because the sauce/cheese ratio is skewed heavily in favor of the cheese, or the crust, even with all that char, is lacking in flavor. It's almost as if they stretch them too thin then cook all the flavor out of the dough. Then they cut it into 12 asymmetrical slices for some god only knows reason, so I can't even give it a good fold.
Denino's is on my list as well. Their entire menu looks really good. I think they opened one in Manhattan.