I really like Flying Fish. With a 4yo, you may want to look at an earlier dinner seating (5:30pm or so). This has the added benefit of being a little quieter. We've taken our daughters here and they have been well taken care of by the servers, especially Bob. It's in the same vicinity as Captain's Grille (on the Boardwalk).
Artist Point over at the Wilderness Lodge is another signature restaurant that is usually not too crowded, puts out some good food, and has an interesting resort to explore around it.
Similarly, Jiko over at Animal Kingdom Lodge, and Sanaa over at AKL-Kidani Village put out some great food and are likewise situated in places where you can explore before or after the meal. Jiko is a signature restaurant, Sanaa is not, but still does excellent work.