I thought I read on another thread that WL also has a bus running to MK? That might alleviate some of the concern you have about the boat transportation to MK. When we stayed at VWL and needed to get to a preopening CP ADR, I remember taking a boat that went to the Contemporary then walking from there.
With MK, the Contemporary with it's walking path gives you the most control.
With the Poly, you've got monorail, boat, and don't forget you can walk to the TTC and take the ferry from there.
As far as which hotel is cleaner, can't help you with that. I think that depends on housekeeping staff. The Poly rooms are more dated and will be refurbished soon, if that makes any difference.
Do these resorts still have availability for NYE? You may end up having to take whatever you can get! However, with the hotels you've chosen, I'm sure you'd do well with any of them!