It depends on where you are at, and what type of gun. You cannot shoot lead shot on any public Alabama waterway, and you cannot shoot a rifle. I am not sure about pistols, but I would imagine they cannot be discharged on the river.
You also cannot legally shoot any gun from a boat if your fueled motor is running or is in motion from the motor (basically, you can't come in at 40 mph and kill the motor and start shooting while still moving).
Also, there are lots of places in lakes and rivers throughout Alabama that it is illegal to hunt - thus fire any firearm (less than 100 yds from a residence, some city limits, etc.)
Basically, I would probably just get away from the snake to be safe. It he starts coming in the boat, just knock him back in with a paddle and haul arse.