Gosh, that is like comparing apples to oranges.
OK-- I will try
Wilderness Lodge- a warm, rustic, cozy place with fireplaces, lots of dark wood, very Native American feel. Rooms here are small for a deluxe resort. A compact resort where the lobby is never very far away. Has 2 full service restaurants, plus boat to either Fort Wilderness or Contemporary to enjoy the restaurants there. Has bike rental and trails that lead into Fort Wilderness. Has bus transporation they share with the Grand Floridian to all parks and boat transporation to the MK. The pool is beautiful with the hot springs from the lobby feeding into it a slide and 2 hot tubs near the geysurs. The geysurs are fun to watch, and you can see the Electric Light Pageant from the pool and some of the rooms. You also have beach here, but you cannot swim in Bay Lake.
Boardwalk- very convenient to Epcot and Disney MGM (walking distance, or take the boat launch), as well as Fantasia Gardens. Access to night life and arcade games with a carnival feel for the kids. Has surrey bike rentals so you can ride the walkways of Crescent Lake. If you want a room that is away from the bustle of the actual Boardwalk, make sure to request it-- the night life can go until 2 am, so you may not want to be right over the restaurants and clubs. Nice pool with nice slide for the kids, hot tub. Access to many varied restaurants, including Spoodles, Flying Fish, ESPN Zone, not to mention the Yachtsman Steakhouse, the Garden Galley and Cape May Cafe at the Yacht and Beach Club, as well as the various restaurants in the Swan and Dolphin. The atmosphere is very turn of the century New Jersey Beach Front. It is festive and lively as opposed to warm and cozy.
As I said, they are very different resorts. Perhaps you might consider spliting your stay and get a taste of each?