[Professor S]

Well lets add it up:

Pirate

Pros:
Parrot
Tattoos of loose women you met in Milan and the Barbary Coast
Swords
Cool outfit
Cannons
Gold Doubloons
A Ship to Command
The Open Sea
Fame
A life of self-defined adventure

Cons:
Fake leg, but that could be cool I guess
Scurvy
Long voyages with no females (bad luck)
Mortal peril from Her Majesty's Fleet

Ninjas

Pros:
Silent killing machine
Cool outfit
Swords
Throwing stars
Nunchukus (well, I would have them, as they rock)

Cons:
Life of constant training
Anonimity
No Cannons (yes, not having them is a con)
Mortal peril from Samurai
A life of being told what to do and who to kill


I honestly don't think its even close. Pirates rule all.

As for the Samurai, a pirate would just Indiana Jones his ass. Samurai comes running with a sword, pirate pulls his pistol and blows him to kingdom come. Then the pirate would say something devilishly clever and get loaded on rum and opium. I repeat: Pirates Rule All.