Take a screw driver, and jump pole to pole on the upper starter solenoid, if it cranks over and the key is in the on position and it has fuel it will start, 20 dollar part from BAM and these things are KNOWN for going bad all the time. Replaced about 4 of them in the baja and the apache needs one now. I carry a spare just in case. If it does not crank doing the pole to pole jump, then you have to start looking elsewhere. When trouble shooting issues like this dont just start swappiong parts hoping for it to work especially since it seems you have to be OUT on the water for it to happen. When it does happen again, Jump the poles, see if thats it. If you do get clicking and the engine does crank, you might have moisture in the distributor cap, Bad or corroded rotor, bad coil as suggested or bad coil wires. You should yank out the plugs too and see if there is any water in the cylinders or if there is any moisture on the plugs, with the plugs out does she turn over nice and easy. (with no compression she will if she turns over at all.
Maybe swap the coils from one engine to the other and see if this problem surfaces on engine #2 if it does you have isolated the problem and can get a new one. Swap the coil wire as well. Dont just start throwing $ at the problem right away, check the obvious first.