You people are totally disregarding one of the most fundamental laws of physics, which is considerably clouding the judgement of those involved in this debate. The law to which I refer is the Law of Inverse Ninja Strength (more commonly known as the Stormtrooper Effect), which states that the strength of any one ninja is inversely proportional to the number of ally ninja able to assist the original ninja. This means that if one hundred ninja attacked ten pirates, the pirates would totally devastate the ninja forces. Likewise if a single ninja attacked ten pirates, the pirates would die almost immediately. Note that in the first case, the ninja forces would only be decimated until their number reached 10, in which case it would be a fair fight. Who would ultimately win the fight (at the "mano a mano" stage, or one pirate vs one ninja) would be determined either by random die roll or by the subgenre of the movie.
*edit* note that a lone ninja is almost invincible, and the random die roll would be considerably weighted against the pirate.
*2nd edit* note that pirate movies are notoriously unrealistic, and that if a pirate ever did kill a lone ninja in a movie it is probably ficticious.