If the water is a mesh that you have control over, you'll have to manually implement the hole in some way, shape, or form. Booleans would be easiest in terms of automation, otherwise just manually knife and/or move the vertices until you have the hole. Another option would be to have a trans map with the shape of the boat hull cut out of it, and then position it on the water via UVs where the boat is...this would only work well (in Anim8or) if you're not using the UVs for anything else, like tiled textures.
If doing animation, then the easiest method in Anim8or would probably be to use morph targets to lower vertices based on the path of the boat.
I'm not sure how much you're doing in Anim8or, and how much you're doing in Bryce, nor Bryce's capabilities, so that's the best advice I can offer.