Of the restaurants that accept the dining plan Flying Fish probably has the best all-around seafood menu at WDW - it's a signature restaurant, however, and you will need 2TS credits if you want to dine there on the plan.
For overall best seafood I think Bluezoo over at the Dolphin is as good, if not better, than Flying Fish. Bluezoo does not accept the dining plan and does not honor any discounts (AAA, DVC, etc). It's an out-of-pocket expense and is on the pricey side, but absolutely worth it in our opinion.
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