If one were to make a plug in for the Archimede's Ships mod (see below for links), this would be one way of facilitating the cross over. A shipwright can be an NPC who provides work to a naval yard control block and as long as this block is fed the required resources from a courier (and its bounds are in a large enough and deep enough body of water) the shipwright will build ships based on designs either found, researched, or created by the player and imported thru the structure scanner.

Mod page for Archimedes Ships: http://www.minecraftforum.net/forums/mapping-and-modding/minecraft-mods/1289952-archimedes-ships-v1-7-banking-ships

Inspiration for ship designs (a couple of worlds present of ships which can be downloaded and scanned): http://www.planetminecraft.com/member/sillouete/