Venice was by far the best. Naples was a dump. I am hella broke right now, but I did manage to see 7 museums + Colloseum, Boboli Gardens & Pompeii (spent 4 hours there).
The best museums were:
Galleria Borghese (Rome) - those Canova sculptures were gorgeous. Lots of great paintings, too. The only disappointment is that Caravaggio's Boy with a Basket of Fruit was on loan at another gallery in Spain. If you are thinking about going to this museum during peak season, you need a reservation as there are capacity restrictions.
Vatican Museum (Rome) - huge place. You need at least 5 hours to see everything.
National Archaeological Museum (Naples) - worth seeing are the Pompeii and Herculaneum mosaics and the "Secret Room" (lots of penises in this room!).
Best to go here before 12 noon, as the Secret Room doesn't seem to be open after 12:30 pm (it was closed right after I got out of it).
Uffizi Gallery (Florence) - again, lots of great paintings, notably Botticelli's The Birth of Venus and Primavera.
I also recommend the Gallerie dell'Accademia (Venice) and Duomo Museum (Florence).
The food pretty much sucked the whole time. I really don't like their food. The food at the airplane was better actually!!
P.S. Italian restaurants in the US do it better.