I like the idea of the Harpooner, but do we really need a new unit to accomplish this? Players are unlikely to build more than one or two, if any. Why not make a Harpoon promotion available to certain units? In any case, if a Harpooner unit is implemented, it should be strong against Beasts and Animals, but weak against other Naval units.
Maybe Lunan ships (or just Lunan Pirates) can start with the Harpooner promotion. When they upgrade the promotin could carry over with them (like the animal handling promo).