Brooklyn,
The good news is that you are going to be happy either way. Both are great dining destinations. But I am glad to weigh in on which I prefer, and why.
Flying Fish Cafe
The setting is both contemporary and whimsical at the same time, if that is possible. The seafood is, in my opinion, the best on property. The non-seafood options are not particularly numerous, but everything there is served with a modern flair and subtle elegance that seems worthy of what you are paying. I also love being able to see into the kitchen, and the fact that when you are done with dinner you are able to stroll the BoardWalk.
Le Cellier Steakhouse
So if they only served the Beer Cheese Soup, I would still eat here regularly. Add onto it a nice selection of steaks and other entrees and you have a great dining choice. I particularly like the Mushroom Filet Mignon, but they do have some other good non-steak choices too. I think the decor can be a bit dark for my tastes, but on a hot Orlando day it can be a nice and cool escape.
BOTTOM LINE: My personal preference would be the Flying Fish Cafe. But if you have one person who doesn't like seafood, and another who does not like steak, Le Cellier might offer a bit more variety. If that is not an issue, I think that Flying Fish will leave you feeling like you dined at a signature restaurant.
Write me back if I can help some more.
Have a magical (and delicious) vacation!