I've been gone from the forums for some time, so forgive me if my memories of the earlier details escape me.
It wouldn't have to be a *literal* Minecraft chest; it could be a *chest-like* part of the boat model. The boat, as an entity, could implement the IInventory interface and provide access to any inventory-management features. Or so I assume.
Perhaps "boarding a ship" (especially one that allows for multiple crew slots) is done in the same fashion as opening a GuiScreen; there may be a role for a commander who sets a long-range destination; a navigator who pilots the vessel toward the destination; a quartermaster who does what the traditional quartermaster does; and so on. Any more crew could be boarding parties and defenders, if you wanted to go the route of piracy or such.
This seems like an interesting idea, but I would honestly prefer building ships out of blocks, as it would make the ships more customizable and allow people to sail ships that they spent large amounts of time constructing.
I think that this is a very good idea. An upgrade would be submarines, which are version of the boat with a hull over the top, and the ability to sink. Although only oars should work underwater, and the skiff should be the smallest submarine.