Jim, how extensive is the repair?
A lot of epoxies will set up just fine underwater the trick of course is getting a "clean" bond to whatever you are fixing. I think I'd be tempted to use a can of self-expanding urethane foam (used as insulation) under a repair mat though. The reason is that urethanes actually ABSORB water as they cure, and the instructions tell you to DAMPEN surfaces before applying them. Which makes me think that if the repair was relatively minor, I'd get a better bond and a patch that was easier to chew off when I did haul. (And conformed better to any voids, etc.)
No way that you can heel over, i.e. put an anchor out the boom or to the masthead, and haul the boat over far enough to work temporarily dry?