Hi Deborah,
This is probably one of the most important decisions in your vacation plan (aside from the time of year to visit), so I understand how difficult this choice can be!
You've done a great job narrowing things down, and based on your list I would pick Bay Lake Towers, without question. This resort boasts beautiful 2-BR villas (with full kitchens, laundry, whirlpool tubs) all within walking distance to the Magic Kingdom. This is a huge benefit when traveling with toddlers and preschoolers. This resort is the newest on Disney property, so everything is updated, new and should be in impeccable condition. Unfortunately this may also make it difficult to secure a reservation because it is so popular.
For your backup plan I don't think you could go wrong with any of your other selections. I love the Polynesian, however they do not have the same amenities as a villa. The Beach Club does have the villas available and I adore the ambiance of the Boardwalk area. It is a great resort for enjoying down-time and relaxing evening entertainment on the Boardwalk. The Villas at Wilderness Lodge are beautiful, however although they are in close proximity to the Magic Kingdom it feels like you are worlds away!
Good luck with your decision, one of my favorite websites for assisting in making my decisions is
www.allearsnet.com They have a fantastic library of photographs of every Walt Disney World Resort.
Hope this helps!