I actually just had this very dilemma, and I think the answer lies more in what you're looking for in your hotel.
I ended up choosing the Animal Kingdom lodge for a couple reasons. First was budget. The Polynesian was somewhat more expensive than the Animal Kingdom Lodge. The view was very important to us. We knew we'd either get a waterview or a deluxe savannah view, and the deluxe savannah view was somewhat cheaper.
Second, I looked at transportation options. While the Polynesian does have the monorail, I had initially planned to rent a car, and use it to get everywhere with the exception of the Magic Kingdom, simply because I hated the process of going to the TTC, getting on the monorail, and then walking to the gates. The busses drop you off right at the gates. Well, with the monorail being the only way to get to the Magic Kingdom (other than a ferry boat), it kind of made that pretty much a moot point. Having a car negated the need for bus transportation, so that really wasn't a concern of mine.
Third, I'm going on my honeymoon, and my fiancée and I have been to Disney World a couple of times together, so we've pretty much experienced the parks. We wanted to have a little bit more time at the resort, and since the Animal Kingdom Lodge is somewhat more secluded, we opted for that.
And lastly, I much prefer how everything is under one roof at the Animal Kingdom Lodge. I don't much care for having a "main building" at a resort.
Another option is to split your stay. Do a few nights at one, and then move to the other. If some good AP rates come out, I may just do that.
Whatever you decide, I'm sure you'll have a WONDERFUL trip. Enjoy!