I've only eaten at 50's PT and Via Napoli. I love them both, so you can't go wrong. I love 50's PT for the atmosphere, playful staff, PB&J shake and Fried Chicken. I would say this is more kid friendly and has more of a theme. I love Via Napoli for the best pizza, not only on Disney grounds, but in general. Via Napoli is also great to sit outside and soak in the atmosphere of Italy in Epcot.
I'd say it comes down to the vibe you want, who is in your group, and where you are coming from/heading to.