Water-skiing is popular all over Florida even with 1.6 or so million alligator in the state. The key is to ski in designated and approved bodies of water. Bay lake is quite safe. You might notice that they don't allow you to launch directly from shore or in the canals, only in the deep section of the lake.
Note: Alligators are not big on open water swimming, they enjoy warm shallow marshy areas that are quiet and have a place to "sun" during the day when the weather / water is cool.
Dave