If you end up at Flying Fish, try the tilefish. It's a not a readily available local fish similar to grouper. Some people have compared it to scallops and lobster. Imho Narcoosees or FF. Either way you can't go wrong.
Kind of a tough call, as many of the WDW spots have several excellent seafood entrees on the menu.
But if pressed, I'd have to go along with the Flying Fish.
This wasn't a "seafood" restaurant, but the Cedar Plank Salmon at Artist Point, Wilderness Lodge was EXCELLENT, and gets my vote for "Best Seafood Entree".