I had a very similar situation to yours. My boat was up on the cable lift, probably 4' above the water, and I started unsnapping the cover. A 6' black snake was RIGHT THERE in my face when I rolled the cover back. He startled and tried to escape into the rod tubes, but he was too big to fit into them, so he was just wriggling right there by the driver's seat. I reached in, grabbed him by the tail and flung him out into the lake.

I was pretty juiced on adrenaline from the surprise of having him pop up right in my face, so I ended up throwing him really, really far. I'm not really scared of snakes, but I definitely prefer to see them before they are close enough to breathe on.

Now I peel back the cover slowly and take a peek in there before I go popping all the snaps off. Haha...