We've stayed at either YC or BC for the past several years. We've finally decided, after going back and forth, that we like the Yacht Club best. Yes, it is a little bit farther from Epcot than the BC is, but when it's really hot, we still enter the BC at it's closest entrance (through the gate) and continue through the BC, winding our way through the lobby and then outside only long enough to go past SAB and B&C, then inside the YC and up to our room. If it isn't that hot out, we just continue down the walkway and in the entrance to YC. It really doesn't take that much longer either way, but the kids (and us) just love that first burst of a/c on a 100 degree August day.
As for the boat dock, yep, it's closer to YC, again it's not very far from either. The BC does have a more informal feel, due largely in part (I think) to people waiting for seatings at Cape May. Most of the time, people don't really have that much of a wait for Yachtsman's. Thus, no one is really sitting around right outside the restaurant, plus, the entrance to the restaurants at YC are a bit further down the hallway from the main lobby, not right in the main lobby like Cape May at BC. Now, I will say, the solarium at BC is awesome and can be very peaceful and quiet, um..... unless there are 12-15 kids playing board games and card games like we saw last time. Even then, it's great that they had such a nice place to do so, so we just went to relax in another quiet area (I'm not telling where... it's our secret)

.
Much larger gift shop (especially since the renovations at Atlantic Wear) at BC than at YC, but you can still get soda and such at YC's.
It all comes down to personal preference. Both are lovely resorts and both will be very enjoyable. I guess if you really wanted to compare you could split your stay...I've never heard of anyone splitting it between the two, but, hey, it's Disney World, anything goes

. Hope you enjoy your stay whichever you decide on!