Well lets look at the pros and cons of each.
Pirates.
Pros:
- They have guns. This is self-explanitory.
- They have ships with weapons. Canons mean businuss
- They don't have morals or honor. Anything goes.
- They have guns dangit.
Cons:
- The majority only has one eye. If your enemy relies on stealth, then one eye would not do you much good at all.
- Peg legs do not serve well against a nimble enemy such as the ninja.
- Once they run out of ammunition they are stuck with the short-ranged scimitars, which, although powerful, are no match for the long reach of the katana.
- They use 17th century pistols, which aren't exactly the most reliable gun. Of course it is a gun and the enemy doesn't have one, so this is debatable as to whether or not it is good or bad.
Ninjas
Pros:
- They are expertly trained in stealth. When your enemy is drunk and missing an eye, this is extremely useful. Also a good defense against guns.
- They have the element of surprise.
- They're nimble and agile. Of course this is no match for good aim, but if the gun screwed up or if the pirate ran out of ammo then this would be a valuable skill against someone without any legs.
- They have shurikens. And thats cool.
Cons:
- They don't have guns.
- Once they have revealed themselves they are screwed.
- Mainly because they don't have guns.
- Their shoes are basically thick socks. If I was on a pirate ship with only socks on I would be worried about nails.
- Of course I would be more worried about the fact that I didn't have a gun.
Final Verdict
If the ninjas can manage a successful sneak attack on all the pirates at once then they might have a chance, but if not then they are kind of screwed because they don't have guns. So my verdict is Pirates.