I was fishing late in a lake here in Indiana that I've heard has Muskie (but I've never seen one before) and we saw something swimming like a snake that was about 3.5-4' long.  I thought at first it was a big snake, but then it disappears and something hits the water like a baseball bat right in front of the lily pads, then blasts the water two more times back in the pads, and again a few minutes later about 50 yards away.  

 

Would that be a muskie?  I've never heard a fish hit the water that loud before.  

Did you get a good look at it?  The noise you describe makes me think beaver.  Years ago, before I'd ever been close to a beaver slap, I spent over an hour after sunset chasing what I was certain must be the biggest bass in the lake only to finally discover that I was following a dang beaver

If you got close it it, it could be a beaver warning this nest mates about a potential predator. Beavers slap the water with their tails to warn other beavers.

I'm thinking beaver as well. 

I know there are beaver there, but we heard a beaver there a few weeks hit the water, I didn't think the noise was as much of a flat slap.  Plus beaver don't swim like snakes.   Maybe there was a big fish or a snake there and it spooked a beaver?  I really have no idea

*insert Beaver joke here*

Maybe it was a big snake and a big momma was blowing up on it? 

Thats not musky behavior from my experience. Musky on a normal swim do not move in a big S like described. If it was on a pretty good pace then possibly but i wouldn't be so sure.

A beaver's tail would look like a snake when in swimming form. I see alot of muskrats and their tails look like a snake.