You really can't see MK from VWL from the Villa side of WL, unless the hurricanes have changed that since I was last there.
VWL is our home resort, so I'm probably biased, but I would pick it over BWV. With little children in tow, you will probably want to be closer to the MK, and it's just a short boat ride away from VWL. From my understanding the bus service from Boardwalk to MK can be a lengthy trip at times, and I wouldn't want to have to stand there and wait or be stuck on the bus at nap time. JMHO With boardwalk you could walk or boat to MGM, and Epcot. So it really depends on how you will spend your time. If this is more of a resort trip, WL has some great activities and Fort Wilderness is next door with the petting zoo, and pony rides. It all just depends on what kind of trip you are looking for.