I dont know what the point of discussing this is. A ninja would win in a nanosecond. Lets review the facts.
Ninjas can disapear without even trying.
Ninjas can kill without anyone being the wiser.
Ninjas have access to a variaty of weapons, including, but not limited to, throwing stars, poison, naginata, bow and arrows, etc.
Pirates only real ranged weapon is a musket, very inaccurate, and a pistol, same as a musket, and they both take forever and a day to reload.