Well, we haven't stayed at either, but we have stayed at FW and we will be staying at AKL for our January trip. The boat from MK to FW is very nice, but timing is everything. If you just miss it, it might be a while before the next one comes. And it makes a triangle between FW, MK and WL so on on leg of the trip you will have to wait through a trip to FW. A bus might be faster, but the boat is much more fun.
We chose AKL for our next trip because there are supposedly lots of activities for kids...parades in the lobby, storytelling, flamingo feedings, viewing the animals with night vision goggles. Our DD loves zebras and likes to sit with a drink and just observe the zebras at our little local zoo, so we think she will get a kick out of being able to view the animals from the hotel. I have heard that the bus service is very good and there is little to no "bus sharing" so you have a direct shot between AKL and wherever you are going. They are building a new DVC at AKL right now, so there might be some evidence of construction if that is a consideration for you.
I don't think you can go wrong either way. We considered WL for the proximity to MK, but went with AKL because we though DD would enjoy the theming and activities more. Have fun!