We've been to all three, and have a strong preference for Via Napoli.
The atmosphere at Via is light, bright and airy with high ceilings. Our family of five loved the food - and we all have different tastes and appetites. It's rare for all five of us to agree that a pizza is really good. Great caprese salad, good bread and yummy sangria, too. The service was much, much better than I've experienced at Tutto, especially with kids.
Tutto is fine, but after many visits, we aren't likely to return soon. The food isn't much different from local Italian restaurants, the atmosphere isn't as interesting to us and in our experience, the CMs have been less friendly than the average Disney CM.
Coral Reef is interesting with the view of the tank and the theming, and there are a few menu items that we enjoy, but it's not at the top of our list. It's dark, which isn't a big deal, but we prefer the atmosphere at Via or Chef's for a lunch ADR.
Good luck with your decision!!