Remember, waves, including tsunamis, are mostly surface events out in the open ocean, and unlike normal waves, they have a very long period, and before they reach shore, are typically only a foot change in height. Granted by the time it gets to dive depths it is likely starting to rise up towards shore, but it will still be nothing like what strikes land. So I can see how it would be very easy to miss one passing when on a boat, as it is just a gradual rising up to a foot, followed by a gradual sinking.
In fact, when a tsunami is heading towards a harbor, one way boats can avoid being damaged by it hitting land is to just go out to sea a bit, so they only hit smaller swells.
But being in the water during an earthquake, it seems like if there is a loose bottom (sand or silt) that it would stir up the bottom a little bit.