I haven't been to Flying Fish Cafe, but I have been to Narcosees and loved it. The atmosphere is very nice and the location is beautiful....We were seated in a table near the window where we could see The Seven Seas Lagoon and also Wishes from the MK Castle and you could see the Contemporary Resort also its like a panoramic view of that whole area. The food was awesome. My DH and I had the filet migon with the lobster tail, and it was cooked to perfection. Also the service there was awesome, the waitress knew what she was talking about and everything that she recommended from the appetizer to the dessert and the wine was awesome. So i definitely would go with Narcosees.
Based on my dining experience last August, Narcoossee's. Narcoossee's was the best meal we ate out of all the places we went and Flying Fish was the worse. We were extremely disappointed with Flying Fish and don't plan on trying it again any time soon.