Pros:
Boardwalk - much newer, transportation options are a lot better as its kind of central to the entire property, walking distance to Epcot.
Wilderness Lodge - Great Decor, close to MK. Can give you that "in the middle of nowhere" feeling. The main lobby is beautiful.
Cons:
Depending on what your view is at the Boardwalk, you may have to deal with noise if you are facing the water because of all the shops and restaurants below. Everything starts shutting down at 10 but you still have wandering groups of people.
If you are at Wilderness Lodge, you'll have to deal with noise as well, from the MK fireworks. If you are up late it wont bother you, but if you have an early morning, it could be an issue.