Mangrove would be the only thing that comes to mind. They might be unusual but they shouldn't be that hard to find if you actually do some looking. I have seen them sold at some saltwater fish stores, and I'm pretty sure you could get either seeds or plants off eBay. Keep in mind thought the only part under water would be the roots. But I'm sure you already knew that :)

The best way to make an underwater bonsai is to start with a dead tree with lots of branches and add java moss or Christmas moss to the branches for the "leaves" and trim to the shape that you want. I have seen a few of these tanks and they are quite stunning.

I don't know about bonsai'ing them, but these are the trees I know of that grow in water, Water Tupelo, Mangrove, Pumpkin Ash, Bald Cypress, Buttonwood.