Good question but it's a tough answer, rather like asking people if their favorite color is green or blue.

Here is my take on both resorts.
BWV: If you can get over the scary (too some) clown pool, it's a better pool than that at VWL. Further, there are lots of eateries and activities sitting right there on the Boardwalk. Epcot is a short walk away, and DHS is a moderate walk (though some 3-yr olds might consider it a lo-o-n-n-g walk, thus so would their parents

). Given the Food & Wine Festival is going on at that time, getting a BWV room is great if you plan to spend a lot of time there.
VWL: This is a far more serene resort, more intimate. It's also among the best-themed resorts on property. Walking into the lobby alone is a vacation-making experience. There are activities there, too, just not as many shops as you'd get with the Boardwalk. The boats from there to MK are a bonus, as are boats to the Contemporary (thus monorail access and the shops there). The
DVC rooms at VWL were recently refurbished, too. From VWL, you can take a moderate walk to Fort Wilderness where kids can pet animals, etc.
We love to relax at the end of the day/evening, and since that's important to us, VWL is our home. However, I believe either resort would be lovely. Good luck!