We stayed at both, and the good news is you can't go wrong with either choice.
SAB is hands down best pool on property, but the really long slide might be intimidating to a 3 year old..and some 6 year olds too...the "beach area" is great, my kids loved playing in that alot and the slide was a big hit, but they were older 9 & 7 at the time. Walking to Epcot is really great, bus service to the MK is just Ok, and sometimes you share buses with YC and BW. The BC theme might not Wow kids of that age group, as compared to seeing the animals at AKL will.
AKL has a smaller pool area, which has its pluses, if you stay with the younger one while the older one goes to the slide and swims, its more doable at AKL than at SAB. Also I thought the thrill of seeing the animals at AKL would get "old hat" after a while, but it was always exciting. There were also a lot of little things for the kids to do at AKL more so than I had thought.
Both are great resorts have fun with whatever you decide.