We have stayed at both, and they are really hard to choose between.
I think it depends mainly on who is with you. If you have smaller children, and will be at MK alot, then Poly would be the better one to choose because of its easy access with the monorail. When my 2 yr old fell asleep in the stroller on Main Street, we were back in our room within 10 minutes, and didn't have to take him out, or move him at all. If you like to go back to your room alot and will be spending MOST of your time at MK then choose Poly.
However, the pool and other amenities at B&YC and that area are, IMHO, better. Also We love to go to the different lands in Epcot and eat so this is easier here. It just depends mainly on your crowd.
Good Luck.