We've stayed at both and loved both. At BC, we were in a villa, and at Poly, we were in concierge. Of course if I had to choose BC villa or Poly Concierge it would be the villa....seperate bedroom, kitchen, full fridge, etc.
If you are comparing standard rooms from each, then it really depends on the ages of your children, what you plan on doing ,etc.
The BC is walking distance to Epcot which was GREAT! A quick boat ride to MGM as well. I can't wait to go back there again on a future trip. The pool was fantastic and the kids loved it. You can walk over to the Boardwalk, Dolphin and Swan as well so good access to many restaurants.
The Poly has the monorail which is great with a double stroller. Wheel it in with kids and stuff loaded and get off at the park entrance. We had the concierge/beach front, so it was romantic, and had nice advantages to a standard room. The Transportation Center is an easy walk from the Poly, so you can walk over there and get on an Epcot monorail without switching.
Both are nice....just look at where you will spend the most time......MK or Epcot/MGM. That will really be the deciding factor.