Of all the Pirates vs. X permutations that have caught the fancy of the Internet, perhaps the showdown that makes the most sense is Pirates Vs. Cthulhu. Logistically, ninjas are not likely to take to the high sea, where as pirates patrol and plunder the very waves under which R'lyeh rots and Great Cthulhu lays dreaming.
It is an excellent idea for a book, and the Elder Signs Press is now making it a reality with High Seas Cthulhu:
I hope there is a follow-up volume: I would be tempted to write a Herbert West, Buccaneer pastiche.
High Seas Cthulhu [Elder Signs Press]