This is based on some engineering intuition and quick research. I think if you absolutely must put an electric generator underwater, sooner or later the sliding seal on the motor/generator shaft is likely to fail. So that failure mode would be nice to avoid if possible. Here's a solution. Use a motor/generator design like this, even if it means you have to build the motor yourself.
http://www.efficientplantmag.com/2008/09/understanding-canned-motor-pumps/
Put a solid, stationary, waterproof "can" between the rotor and stator of the motor/generator, likely made of a higher-temperature plastic or maybe ceramic. As long as the "can" is not electrically conductive then there won't be eddy-currents causing a loss of efficiency. And as long as the "can" material is as thin as possible (maybe around 0.010" to 0.030" thick), then the magnetic field can pass through, allowing it to work. Note: the thicker this gap is, the lower the motor/generator's power-density will be. It will essentially "de-rate" the motor/generator's normal power rating that would otherwise be expected. Also for better power density gear-up the drive speed *before* going through this "magnetic coupling" and/or use more magnetic poles.