It is obviously the "Ninja". Ninja was only the commoner's word for the real thing, otherwise known as Shinobi.
The Shinobi were masters of the arts of stealth, disguise, thievery, spying, and assassination. Pirates, as they are known, were nothing more than romanticized thugs and sailors.
Should the two want to have a go at each other, the Shinobi would obviously win. The Pirates wouldn't even know the Shinobi were there, for the most part, before they died.
Just as well, Shinobi also had "day" jobs, usually as bushi.