Daniel,
First of all CONGRATULATIONS!
In my line of thought, you need to focus on a meal that is ideal for you and your wife to celebrate your anniversary first, but secondly to choose one that will keep your son content as well. So there are so many good choices, but here are a few favorites;
Yachtsman's Steakhouse: So this location is nice for several reasons. You and your wife get a nicer, fine dining experience that befits the occasion. They have a kids menu, which means they have some selections that should be good for your son. Plus you can enjoy a pre- or post-dinner romantic stroll along the BoardWalk or Epcot World Showcase, and maybe even share in a family celebration ice cream sundae at Beaches and Cream?
Chefs de France: A bit less pricey, but with a more elegant setting. If you are seated along the windows your son will have plenty to distract him. And how romantic to be dining in a French street-side bistro?
I would also consider Be Our Guest (Magic Kingdom), Flying Fish (BoardWalk), Narcoossee's (Grand Floridian), and the San Angel Inn (Epcot), dependent upon where you are and what you like to eat.
Write me back with more about what you like, and we can refine the suggestions!
Have a magical (and delicious) vacation!