I agree that you can't go wrong. I personally would not base the choice on transportation, because I think AKL's bus service was outstanding, and the WL boats can be glacially slow. However, my DS3 does not nap in his stroller...
I think it all depends of your child. My DS3 did love the animals, but really wasn't that interested in them after a couple of days. He's a VERY active child and we could have used some places to let him just run around, which we did not have at AKL. My DS1 however, could have looked at the animals all day long, every day, and doesn't have tons of energy to release.
Good luck!
--mainebound