We've stayed at both the Polynesian and the Contemporary. I'd have to say "it depends..."
If you want the charm of the exotic south seas theming and the feeling of being away from it all at your resort, then go with the Polynesian.
If you want the feeling of being in the middle of the action and right next door (walking distance) to the Magic Kingdom, then the Contemporary is the place for you.
Both resorts have large rooms, great restaurants, and excellent transportation options, so It's really a matter of personal taste in theming.
Just my 2 cents.