Although I don't know the specifics here, and I understand that ignorance of the law is not a valid defense, it seems flat out insane to criminally prosecute the guy.

I give him the benefit of the doubt that they are telling the truth and this at least started by bailing rainwater out of a boat. That's a very normal activity, no reason to presume that any harm could come of it.

Then, first bucket gets tossed in and he sees that big splash. It's Florida, so there could be lots of potential explanations. It might be bigass catfish. It might be alligators. Could even be dolphins, depending on where they are in Florida. ...And, it might be manatees, although that probably wouldn't be the first thing I would think of.

So, big splash. I'd be surprised. My first reaction would be: "I wonder if it will happen again after another bucket." NOT "Oh dear, perhaps I am frightening some poor defenseless little creatures and should immediately cease what I'm doing." If I came the the conclusion that it was gators (which seems more likely/reasonable than manatees to me, although I don't live there), it would even stand to reason that frightening them off would be a good thing to do -- encourage them to move away from populated areas.

Given all that, it seems very unlikely to me that the dude had any malicious intent. If he knew they were manatees and knew that stressing them out like that could negatively impact their health, perhaps punishment would be in order. But if he thought they were anything else (fish / gators / whatever), or just plain didn't know, continuing to bail the boat in an attempt to get whatever they might be to swim away seems like a very reasonable thing to do.

Educating people that "hey, if you see something like this happening, it might be manatees and you should try to avoid stressing them out" seems like by far a better and more rational option than "throw the animal torturer in the slammer!"