oh pleanty, I am currently running a Swachbuckling game, a little different but not too, and have some ideas for you that are a little off the beatend path
1) A thaumaturge from England wants to investigate reports that magic works in the New World and figure it all out. This plot element is in On Stranger Tides to some degree, but you could alter it.
2) There are political dealings afoot in the new world, and a privateer is more than just an oportunist. He is looking for something specific that England/Spain/France has that would shift the balance of power in the new world and the old.
3) A destraught young woman hires the PCs to rescue her brother who has been captured by a gang of pirates. Whether he is a prisoner or a new recruit is unclear.
4) The PCs join a rebellion to create a True Free State in the New World, a home for ex-slaves and pirates and anyone else. They can work their way up from small time raids to being govenors.
Thats just a few.