We did the POLY last May and WL in December and absolutely loved both. Know that you won't make a wrong choice

!
BUT, with two young children, I'd opt for the POLY for the transportation alone. My children's favorite ride IS the monorail and I agree with the poster above that the boat ride seems much quicker from the POLY. You can also walk to Ticketing & Transportation Center from the POLY. AND, during meltdowns at MK, you are a quick monorail ride away from your own private hotel room!
I believe Poly has 24 hour food court - my ONLY complaint with WL was that we are late night people and the food court closed rather early.
I don't know if you are driving or flying in but if you do have a car and choose to stay WL, know that driving your car to the parks is a viable option. We used to always take Disney transportation (love monorail and boats but LOATHE the buses - i'm just not patient enough). However, during our recent stays at AKL and WL, we drove to the parks and had very good experiences. IMHO, Disney does a much better job operating the parking lot trams than the buses.
Have a magical time, whatever you choose! Truthfully, you can't go wrong with either resort!
