Easy - go deep. No rocks to smash. Make it a big vertical floating pile - like a buoy but big. Glacier strategy - more under than above. By being vertical, any size wave can come at it and it just bobs up and down. Contrast with a river barge - that flat surface can't handle any waves at all or it capsizes.

Noah's ark might not have been a boat. I'm not asserting anything - idk. But its interesting that the interior design was so similar to the interior of the temple in Jerusalem. One could say that any temple is an ark, since it should be a holy place set aside from the insanity of the world. And that insanity seems to flow in waves, so it could be likened to a flood. Just thoughts, not saying it didn't happen.