We've stayed in both recently, and its a tough choice. We had a wonderful lake view room at WL in Dec. 2002, before we had our DS in the following April. The holiday decorations were incredible. I personally like the theming there better than any other resort.
We stayed at the Polynesian last August with our 18 month old. It is a beautiful place - the pool, the grounds, the atmosphere. It's on the monorail, so access is no problem.
My favorite is WL - in fact, we're going back in October - but the Polynesian is wonderful, too.