There's not a lot of difference between the YC/BC, mainly the theming. Seems to be that the BC has more of a family seaside resort feel, while the YC is decorated with more of an upscale Yachting motif. They both share the pool and you can easily walk back and forth for the restaurants. BC will put you closer to the entrance of Epcot by a few minutes, while YC will get you closer to the marina. Not all YC rooms have a full balcony, but the majority do. There are some rooms on the 3rd floor that have standing room only balcony. BC has fewer "full balcony" rooms.
Boardwalk puts you right in the middle of the action. Just outside your doors are numerous restaurants, shops, clubs and entertainment. It seems to be a very lively place. You're nearly halfway between both the Epcot entrance and the MGM entrance, so you could feasibly walk to both in about 15 minutes.
Unless you have a preference for location, I think you should just pick whichever theme interests you the most.