In turtle fungal cases, you can add a small dose of aquarium salt to the water - this might be an option but I have no idea how salt-tolerant alligators are.
You could also try taking the alligator out, trying to wipe the fungus off and drying the skin, and applying a reptile Iodine treatment (such as Tamodine or Betadine).
Another turtle-fungus treatment is dry docking, where you put the animal in a dry container with a basking light, forcing it to bask and stay dry for 1-2 hours a day. Again, not sure how useful this would be for an alligator as I have no experience there.
Best,
Paul