Sure, there are several ways to do this. I think in most cases a non-fixed tripod would work fine. Keep it lashed to the deck with the deck bungee, then set it up to shoot by simply placing it on the deck. The Joby Gorillapod SLR-Zoom ($55; joby.com) has flexible feet so it can be made to conform to nearly any surfacea kayak deck, rock, or tree. Its made for SLR cameras and camcorders, so it can support a fair load. And so long as the boat is not rocking a lot, it would be fairly stable.
The alternative is to get a tripod that has a clamping base that could be attached to the lip of the cockpit. Or perhaps you could come up with a device that attaches to the boat deck with bungees, and that then can hold the clamping tripod. Adorama, a catalog and online camera seller, markets what it calls Clamp-Pod Table Top Tripod ($40; adorama.com), which is basically a C-clamp with a tripod head. That would give you a nice, secure connection the boat. The one drawback is that its kind of, well, short. Get a Bogen 3007X Tripod Extension ($22; bogenimaging.us) and all will be well.