Here's my suggestions:
MK:
Peter Pan
Winnie the Pooh or The Little Mermaid
A character meet and greet or parade... that way you know he'll have a good view. The parade FP won't open up until closer to your travel dates (assuming you're not going in the next few weeks), so you may want to pick an extra one just in case.
Epcot:
Won't really need them IMO, as he's probably too little for most of the e-tickets anyway. Maybe a FP for Illuminations so he has a good view of the show?
HS:
Toy Story maybe? (check the height requirements)... if not, there's always Fantasmic, and there are (I think) one or two shows that you can FP.
The Little Mermaid would be a good one to FP here, because the effects are awesome, but I can't remember if that's tier one or tier two.
The Great Movie Ride or Muppets 3D might be good as well... they don't generally get crowded, but with a little one, having a FP still might not hurt.
AK:
Any available meet and greet (I think you can do a FP for Mickie and Minnie)
Kilimanjaro Safari (pretty sure there's no height requirement here, but I could be wrong)
Honestly, you may just want to take my list and go down the line and see which things I've listed that he's tall enough for lol... same thing with anyone else's suggestions.
Have fun!