Definitely do Magic Kingdom if you only have 1 day. If you can afford it, I highly recommend booking a Priority Seating reservation for one meal at Crystal Palace with Winnie the Pooh and Friends.
Measure your son -- if he is more than 40 inches tall (in shoes) and a bit of a daredevil, then he will love Splash Mountain and Big Thunder Mountain Railroad as much as my three year-old did last week. Definitely get fastpasses for these as early in the morning as possible. If you've got a baby, ask a CM when you get fastpasses for a Baby Swap Pass and you could ride the ride with your son and then your DH could ride it with him.
My son also loved the Buzz Lightyear ride, Philharmagic, It's a Small World, Country Bear Jamboree, Dumbo, the Winnie the Pooh ride.
Use fastpasses as much as possible in order to avoid waiting in lines. Also, take a lightweight stroller -- we didn't take one for DS and he was exhausted at the end of the day and kicking his baby sister out of her stroller (DH got to hold the baby a lot).
I hope this helps!