The boat makes me motion sick. If I'm at Epcot, I always walk if I'm going to Beach Club, Yacht Club, Boardwalk or Dolphin. I'd probably walk to Swan, too, although that would be the farthest point from Epcot.
If you're at Epcot and you take the boat to the Yacht Club/Beach Club stop, I think you would have to backtrack to get to Cape May Cafe. (But I won't bet my life on it, since I avoid the boat.) If you add up the time spent getting on the boat, taking the ride, getting off the boat, and walking from the boat dock to the restaurant: I think it might be faster to walk.