I've stayed in both and they were both fabulous.
Yacht Club has the perk of having access to Stormalong Bay as well as a beach. It is also connected to the Beach Club which offers access to additional amenities in certain ways I guess. We had a corner room water view and it was really breathtaking. We had a view of the Boardwalk, and it was really neat!
Boardwalk Inn, is for some reason, more charming to me. I'm a sucker for the Boardwalk though, so perhaps I'm biased. But the Boardwalk has the perk of having a nightly entertainment complex right there, which we tend to like. Also the rooms at BWI are extremely well decorated...very pretty. And, if you can get a Boardwalk view, that is really fun too.
So it's a tough toss up. We really loved both, but it really depends on what your preferences are. If it were me, I would lean just a teeny bit towards Boardwalk Inn because it's charming, love the entertainment, and watching people on the BW. But my husband would probably say Yacht Club because the views are great there too, there's a beach, and he's a sucker for Stormalong Bay
Have fun...you can't go wrong!