I would stay at the Poly. Love WL, in the winter. It will be hot in September, and you can pop onto the monorail and be back at the Poly pool in 5-10 mins, with a view of the castle. The boat ride to the WL is nice but a little longer. Also, you can get to Epcot and MK easily via monorail without taking your child out of their stroller. If the smaller boat comes to pick you up at MK or you need to take the bus back from Epcot and your child is asleep in their stroller, you will have to wake them up to fold the stroller up. I always found that to be a huge pain in the neck. Also, the ambiance of the Poly is just amazing and you can watch Wishes from the Poly beach.