Technically the Fantasia buildings are the preferred location (cost $10 extra a night), and they should be the closest. We stayed in Toy Story last year, and it was only a 2-3 minute walk for us..some of the TS rooms were closer than some of the Fantasia rooms, just depneds on where in the section you end up. We were on the far end of the Buzz building, and it wasn't a bad walk at all (With a just under 4-yo and a 15mo old even!).
I'd try for Toy Story, especially if that's your son's favorite. My now 4-yo remembers quite a bit about our trip, and he talks about his TS hotel as he calls it.