I had this same arguement with my brother awhile back, and while Ninjas was winning, I still sided Pirates because:
A) They have guns
B) Rum, do I need to say anymore
C) They do not fight by the rules, where as the ninjas have a code of honor they must abide by
D) They have awesome hats
E) There is nothing like the spray o' the sea in your face me hearty, argh
F) Pirates were recently on the news for highjacking a cargo ship
Now, ninjas do beat pirates in a number of areas:
A) Stealth
B) Going with the Stealth, they wear black and are quiet, as opposed to noisy sterotypical pirates
C) Shurikens
D) Agile
E) Masters of the Blade
F) THEY ARE LIKE THE F***ING JAMES BOND OF THE ORIENTAL WORLD.
So, six reasons why Pirates rule, and six reasons why Ninjas rule.
I side with PIRATES!!!