I'm not sure I understand your problem. Why not land and stick a portal down and have your base somewhere safe and just teleport in for the fight?

Maybe something that would make your life IMMENSELY easier, is to put it right on the forehead of the skull that spawns Bonemass. It would never get destroyed. Getting up is also easy if you stick to stone instead of wood (to make it unlikely to get trashed in a fight).

With that approach, you can just ram your boat in anywhere where it seems half deep enough and be done with it.