I had an awesome burger at Sanaa at Animal Kingdom Lodge-Kidani village this past December. It was delicious! Had a few toppings I am not used to like pappadew goat cheese and some kind of darker mustard sauce. I gave it a try and was not even remotely disappointed. In fact even the other guests with me thoroughly enjoyed thier entrees at Sanaa and the animal viewing from our table was an added bonus! If it isn’t too out of the way I would check the Sanaa burger out for lunch (don’t think they serve it for dinner?)!
Boathouse definitely has the best we've ever had on property, but Deluxe Burger is a close second. I had the southern burger with pimento cheese and a fried green tomato and it was delicious. My husband also enjoys the burgers at SciFi. They are good, but they don't usually cook them to your temperature preference (medium rare for us) so they tend to be overcooked.
I agree with the previous poster who said the lobster burger at the Grand Floridian Cafe. It's the very, very best burger I've had at WDW (although to be honest, I've not had many...usually only at SciFi), but the meat tasted like a REAL burger, and not like fast food patties. It was delicious!
Sit outside at the Boathouse for lunch and get Gibson's award winning burger. Have it cooked as you wish and enjoy both the scenery and the burger. Both are great.