Hi Mandy:
Both Resorts, the Boardwalk and the Polynesian, are amazing Resorts and great for kids. Since you are spending a day at each of the Parks, both Resorts have awesome transportation options. Polynesian Resort is on the monorail, so you have quick access to Magic Kingdom and Epcot. And since Boardwalk Inn is in the Boardwalk Area, you can walk to Epcot and either take a boat or a long walk to Hollywood Studios.
I'll be honest, I was nervous about staying at Boardwalk at first because the pool slide has a giant clown head on it. I thought my kids might have been intimidated by the giant clown, however, they LOVED the pool slide and slid down it over and over.
It's a really close call, and you won't go wrong with either choice. If you choose Boardwalk, your kids may enjoy strolling along the
Boardwalk area, especially early in the evening when street performers, like magicians, come out to entertain guests.
Enjoy your vacation.