Our middle son (a pre-teen) is a self-proclaimed Disney mac and cheese expert and plans to start his own mac and cheese blog after our next trip! I have not personally tried much mac and cheese at Disney, other than the adult mac and cheese at Chef's de France (excellent!) and the stouffer's type at Liberty Tree (not excellent, in my opinion!) But he thinks that the mac and cheese is not the same everywhere at WDW. His favorite is the mac and cheese on the kids' menu at California Grill, which he calls the best mac and cheese not only at Disney but at any restaurant. He also likes the mac and cheese at Garden Grill quite a bit. He ranks the mac and cheese at Liberty Tree and 50's Prime Time somewhere in the middle.
Hope that helps!