Such big decisions & all your choices are all wonderful. They will each provide you with a magical Disney experience, so I don't think you can go wrong.
The Boardwalk: From here you are a short walk to Epcot & a bit longer walk to Disney's Hollywood Studios. There is also a boat system that runs between the resort & those parks. Since there are other resorts located nearby, it does make several other stops as do the buses. I will share with you that we didn't like the many stops, but we loved the proximity to Epcot. If you enjoy activity, its location on the Boardwalk is perfect.
The Villas at the Wilderness Lodge: I like to think of this resort as the quiet resort. It is nestled in the woods & surrounded by nature. A bubbling spring is actually located in the lobby of the main resort. It is a short boat ride to the Magic Kingdom. You can get to the other parks by a bus that is typically shared with the Grand Floridian resort. If you are hoping for some tranquility, this is a good match.
Bay Lake Tower: One of the newest resort, staying here will place you within walking distance of the Magic Kingdom, or you can take the monorail. You can also take the monorail to Epcot (after making a transfer). It is sleek & modern in its decor. It will be the only one bedroom vacation home with TWO bathrooms.
Ultimately, I'd study the links and see which design fits your style best and ask yourself if you would you like to be closer to the Magic Kingdom or closer to Epcot/Disney's Hollywood Studios? Do you want to be in the action or would you like it quiet?
Please let us know if you have any more questions, especially for such a grand trip!