I think a lot would depend on where you plan to spend most of your time. If this is a trip with 4 adults, no kids(?), Boardwalk might be better. You'll be within walking distance to Epcot (a boon if you like to eat in the World Showcase restaurants), and a short walk or boat ride to the Studios. And aside from the restaurants and whatever night life still exists at the Boardwalk District, you'll also have the restaurants and lounges of the Yacht Club, Beach Club, Swan and Dolphin within walking distance.
Wilderness Lodge, as you know, is a little more secluded, but there is a walking path and internal bus shuttle to Fort Wilderness so you have access to THEIR amenities. There are boats to the Contemporary, which puts you on the monorail to Poly & GF (as well as MK naturally). If you're traveling with kids, especially young kids, I'd give the edge to Wildernes Lodge. But if you're not, probably Boardwalk.