NO!!!!!!! NO!!!!!!!! NO!!!!!!!!!!!!
There are no alligators in WDW.
And no sharks either.
Sorry to be the bearer of bad news, but there are over a million alligators in Florida, and they are in almost every body of water at WDW.

This topic comes up at the DIS all the time, and I rememeber someone posting that during the triathalon, they set a course of buoys and have boats with CM's to watch for alligators when the swimmers are in the water. Alligators, unless fed by humans, are afraid of them. So, you most likely won't see them unless they come out on a regular basis because they know food is available. Also, Disney has a policy to leave the smaller ones alone.
As far as the bacteria, I read here that it is sort of "sinks" to the bottom of the lakes, so if you get on a boat at a dock and don't touch the bottom of the lake, you probably won't get sick unless you somehow stir up the depths. HOwever, as someone walks into the lake from the shore, they do stir up the bacteria.
