Going by what the Unofficial Guide to WDW says, at the Boardwalk Villas, you're getting a location near to many other resorts & restaurants and even walking distance to two of the 4 main parks, and I think the studios are the largest out of any of the DVC studios, but you're also in a busier, noisier resort area that could hamper any romantic vibe.
With the Wilderness Lodge Villas, it's a little more secluded (which *I* would find more romantic), you get ferry service to the MK, depending on the time of year you may even have ferry service to the Contemporary which would give you monorail access, and a brief walk or bus ride to Fort Wilderness and all there is to offer there (Hoop De Do, romantic carriage or hay rides, campfires and movies under the stars, granted, they're Disney movies but I always like outdoor movies, myself).
If it weren't a honeymoon, I might be more tempted to do the Boardwalk between those two DVC options. But for the more serene locale alone, I'd do Wilderness in a heartbeat. I'd even consider OKW & SSR before Boardwalk for a honeymoon. They're both more spread out, more secluded, but with ferry access to DTD & Pleasure Island. SSR even has a walkway to the DTD on both ends, and I've heard OKW has a walkway now, as well, don't know if that's definite or not. So you're reasonably close to some night life options without being right on top of them, literally.
And since it is a honeymoon, if you are getting a studio, think about upgrading to a 1 BR for at least a few nights. It gives you an opportunity to get some laundry done without interrupting touring (or anything else, meow), plus you get king sized bed & the larger bathroom with the whirlpool tub (double meow)