Hi Elaine,
You certainly are faced with a tough choice deciding between two incredible resorts. By the looks of things, I'm guessing you've narrowed down your decision to the transportation difference. If so, I believe the Polynesian wins. The monorail and/or boat ride to the Magic Kingdom is short (5-10 minutes); typically, the wait for the monorail or boat to arrive is not too long. You also have the bonus of being able to walk to the Ticket and Transportation Center from the Polynesian to catch the monorail to Epcot (about a 10 minute ride).
The boat ride from the Wilderness Lodge to the Magic Kingdom is also around 10 minutes, but the wait for the boat can sometimes be long. To get to the other parks, you will need to take a bus. The bus ride to Epcot is about 10-15 minutes.
Ironically, the resorts share buses to both the Animal Kingdom and Disney's Hollywood Studios.
If it helps, here are a couple of other little differences between the resorts that you may not be aware of:
WL: The rooms are all within one building; good when raining. It has a jacuzzi while the Polynesian doesn't.
Poly: The rooms are larger. In fact, some of the buildings have some of the largest deluxe resort rooms in WDW. You can have views of the Magic Kingdom or can easily walk to the beach to watch them, too
Regardless of which resort you select, they are both wonderful that I would love to visit again and again!