Hi Andrew, no answers here, but shared desire for an underwater generator.
Have you seen idenergie (canadian).
http://idenergie.ca/en/features/ They must have solved the issue.
I am building a raft turbine, which will sometimes submerge, to make 100w. Plenty of generators are available from china e.g.
http://www.ten-high.com/productsinfo.aspx?productid=197#.WnGY_0x2udt which I am buying.
I'm going to find a waterproof housing (a box), and run the shaft into the housing via 1 or 2 marine bearings. Not quite researched that bit yet.
I'm looking at
http://www.directindustry.com/prod/thb-bearings/product-57112-597289.html or something similar.
Here's a link to my raft (so far):
https://photos.app.goo.gl/ZbuyLEK9pc25nN4D2
Best wishes,
Steve