We always enjoy Cap'n Jack's at Downtown Disney. The food is great, and you can't beat the view.
Not really a seafood restaurant, per say, but Spoodles (at the Boardwalk) has a wonderful fisherman's chowder that I think was one of the best dishes I had on our last trip.
I also had some wonderful seafood dishes at the California Grill (in the Contemporary Resort). They also have a sushi chef and some fabulous sushi appetizer plates.