Recently some people I know started discussing whether a ninja could kill a pirate or vice versa in open combat.  I started to think about this rationally, and my conclusion was that the ninja would be victorious.  Here's why.

The Pirate was a generally untrained but battle harty fighter, very spirited and conditioned to fighting through constant work and combat.  He could be considered the marine of his day, very tough, powerful, and formidable.  His specialty is the high seas. 

The Ninja was trained in the art of stealth, deception, subterfuge, and assassination.  His weapons were his mind, and sometimes a sword or throwing stars, though it varied depending on what persona he adopted.  Though they weren't focused to combat, their training made absolutely sure they were ready if a situation went down.  They could reasonably be compared to CIA agents. 

Should the two meet on an open field in broad daylight during "proper" dueling conditions with their choice non-ranged weapons, I would consider these combatants equal, but if it was a war between some pirate and ninja kingdoms, the ninjas would be victorious, because this would be their forte' to destroy their opponent from within. 

So that's my opinion on the confrontation between these two venerable professions.  What are your thoughts?