Having him use a potty chair with a plastic liner so there is no water in it and it isn't connected to the sewer system where he may be afraid the alligators live would probably be where I would start.
I might also assure him that there are alligator excluder gratings in the sewer lines on every regular toilet that you or anyone you leave him with would ever ask him to use, even when you are out in public, so there is zero danger to him of an alligator attack while on the toilet.
Just out of curiosity, any idea where he heard about alligators living in toilets or sewers?
