We actually just bought tickets to Europe, and I'm researching the same! Naples will likely be a 1 to 1.5 day stop for us, and the places we're planning to visit so far are these:
Da Michele on Via Sersale, 13 - Neapolitan, only Margherita or marinara
Di Matteo (Via dei Tribunali, 94 - Visited by Clinton, and only a few Euros for a whole pizza.
Pizzeria Starita, VIa Materdei, 27, 80136 - Montanara Pie (fried Neapolitan style pie with smoked mozz)
We've got some more research to do where to hit, but from Reinhart's American Pie book and the Serious Eats guide to Naples, these places made our list so far...