Since an earthquake is two tectonic plates moving along a fault line, you'd have to be close to a shore line to feel it. The energy release is along the fault and I can't see how it would be sufficient to churn up thousands of feet of sea water. It is the same as with tsunami - one could pass right by you at sea and you won't know it because the large waves need shallow water in order to build up. The energy "wave" is below the water surface.
I think your friends felt the ship shake from normal interaction with the ocean and nothing more.
As to Puerto Rico having daily quakes, that is quite common in many countries which are on or near the edges of tectonic plates. Costa Rica has several per day according to a tour guide we had there. It's just that they are so small they are only noticed by a seismograph, which is the case for Puerto Rico.