Hi Cody. I can tell you're a fishermen :-) You make good points. Cold blooded animals stay clear of warmer waters. They also avoid objects - like propellers - that may do them bodily harm. Alligators on the other hand feed when they are hungry - which is all the time. Although the alligator is a predator, he doesn't target one particular food item. Instead, he will stick to an area where the gettin' is good. For the most part they try to avoid humans.
People dumping pet alligators or Piranhas (like in Pymatoning Lake several years back) is totally insane. They are humane enough not to kill the animal but to stupid to realize the danger they put innocent people into.
Chemical contamination of any water source is illegal and totally immoral. Should you know of a case that has not been reported then I suggest you speak to your parents about it. Chemical or toxic contamination can alter an animals genetic code and cause it to mutate but this takes a generation or two. It is not an over night situation. It could be true that there is some prehistoric animal lurking in the waters and has been undetected for centuries. People ask how it could go that long without being detected. Well, look at it this way. He knows how to protect himself, he has been at it for years. He is trying to survive.
Now go to the extremes, what if it is a monster? Well, for all the monsters reported in our world, none have ever been caught. If caught, they turn out to be a species we didn't know about, a mutant or something like the giant squid - to big to live in areas that are populated.
A web that you may enjoy Cody is this: http://www.cryptozoology.com/sightings/sightings.php It explains and shows pictures of various crytids. If you are on Facebook or My Space then look up Rosemary Ellen Guiley. She is a known expert in the field. Monsterquest could make a stop in your area, you never know. There have been several notables in my area as of late. GAC with Zak Bagans and then Ghost Lab were just here to film for next fall. Since the number of these shows have increased and their popularity has soared, many are looking for new, before unknown, areas to investigate.