Lauren:
To me, it comes down to the
Beach Club and the
Polynesian. Both resorts offer a fabulous pool, Character Dining, and nearby access to theme parks.
Beach Club's pools, with their sandy bottoms and fun child's sand area, give a parent the best of both worlds: fresh water with castle-building! You can also bring a see-through inner tube and float through the connecting pools as you would a lazy river. It's proximity to the Boardwalk with clowns and nightly viewing of Illuminations would be a good fit for your 3-year-old as would its Character Breakfast at Cape May Cafe featuring Minnie, Donald, and Goofy.
Polynesian's pool sports an erupting Volcano and the resort holds a torch-lighting ceremony nightly complete with drums and a fire-dancer--captivating for young ones in the crowd. What gives it a slight advantage over the Beach Club is its monorail access to Magic Kingdom and Epcot versus Beach Club's boat access to Epcot and Disney Studios (although you can walk faster to Epcot from BC). Its Character Breakfast with Lilo, Stitch, and Mickey is a favorite as is dinner at Ohana with its coconut races that even your little guy could do.
If you think you'd spend more time at the Magic Kingdom versus Disney Studios with your son, Polynesian would be the clear option. If you're wanting to spend as much time out of the park as in the park, I'd strongly consider Beach Club.
Wishing y'all a magical vacation!
Whitney