I've been to both. Blue Zoo is definitely trendier and flashier than Flying Fish, but I think Flying Fish is better. The prices are similar (although I think BZ is a little more expensive than FF). The food at FF is great.
At BZ, if you're not careful you can end up eating dinner with a bunch of people attending conventions eating on expense accounts. They're loud, can be obnoxious, and the guys are usually focused on hitting on the female convention attendees. That's what I tended to observe (my wife and I stayed at the Dolphin for two weeks in October... saw several conventions come and go). The atmosphere at FF was a little more Disney and a little more fun. If you don't care about that, by all means BZ is a great place to eat.