I'm a DVC member and have stayed at both resorts. I've stayed at Boardwalk several times and will be staying there again next June. I just stayed at Beach Club this past June. My thoughts....
If you will be spending a lot of time at EPCOT, you can't beat the quick walk form Beach Club. Yes, Boardwalk is right there as well, but the Beach Club is that much quicker. That is especially nice if you plan to go to dinners in EPCOT. You can make a quick return after a late night of eating. Other than, that only advantage to Beach Club that I would cite is the pool. I did really enjoy the pool, and you can only go there if you're staying at Beach Club.
I happen to like the atmosphere of Boardwalk more than Beach Club. Obviously, this is personal taste, but I'm not too fond of the Beach Club decor, and happen to really like Boardwalk.
The truth is, if you stay at either location, you have all of the same amenities available to you. You can't really go wrong unless you specifically want to take advantage of Stormalong Bay (Beach Club pool).
I'm sure other people will have some helpful ideas. But bottom line, they're both convenient locations to EPCOT and Hollywood Studios. You'll probably be happy with either choice.
(Did I make you more confused?)