I personally prefer the Yacht club. It may be because when I was younger my family always stayed there, but it is my favorite of the three hotels. Really, by choosing any of the three, you are in what I consider the best location at Disney. You are right in the middle of two of the theme parks, MGM and Epcot and have access to all the activites at the Boardwalk.
I find the Boardwalk to be a very nice place to visit and stroll along and it has some beautiful interiors, but it just doesn't "speak" to me :lol: I find the Yacht and Beach club to have excellent restaurants, including my favorite place at Disney, Beaches and Cream. It also has its own "waterpark" complete with a great shipwreck slide, two whirlpools, a "lazy river" and several connected pools with sand bottoms that go underneath and around rock formations, bridges, windmills, etc. The pool alone makes these two resorts the better between Y&B and Boardwalk (and you still have access to the shops and restaurants at the Boardwalk with a short walk).
So, for me, the question would be choosing between Yacht OR Beach. The Beach club is a lighter, brighter, more fun atmosphere from the lobby to the rooms. (Take a close look at the wallpaper, the hidden Mickey's are EVERYWHERE). The Yacht club is much more formal, darker and has an almost "serious" atmosphere. Now don't get me wrong, it is still just as fun as the beach side, after all it is a Disney resort
So for my final thoughts, choose either the Yacht Club or Beach Club. Here you will have access to everything Y&B has, from their pool, to their fitness center, to the great restaurants. Yet, you can still walk around the small lagoon and stroll the shops and restaurants the Boardwalk has. Which, to me, would be the main reason to choose Boardwalk over Y&B anyway.