Kristin:
I would narrow your choices down to Caribbean Beach and Wilderness Lodge...
Caribbean Beach would be a strong choice if you're going in warm weather and will optimize some pool time, as it has a pirate-themed pool and a kids water play station with water canons, small slides, sprayers and the like. A preferred room will get you a pirate boat bed (I hear the mattresses are a little uncomfortable, though) and carpet that looks like wood planks. The cons of the resort are its massive size which requires several bus stops and a few of my friends informing me that their recent stays came with rooms that smelled musty...
If you're willing to upgrade, I think Wilderness Lodge offers superior themeing. The stories-high fireplace welcomes everyone to the expansive lobby and a meal at
Whispering Canyon Cafe is a must. The rooms are a bit larger than CBR and the pool has a geyser and slide. Your son will enjoy the boat ride to Magic Kingdom as its an attraction unto itself. A standard woods view is just as good as a view of the pool in my opinion here, so save your money to get it more in line with Caribbean Beach Resort for your final choice.
Wishing y'all a magical vacation!
Whitney