Take a look at this article and ponder it. If firearms, etc. aren’t an option for carrying on ships, what about non-lethal weapons? Many of them would likely be relatively cheap and quickly mastered by crews.

Indeed, Israeli “skunk spray” mixed with water from a fire hose would be especially insidious since the wife (wives?) of a freshly doused Somali pirate wouldn’t “open up their treasure chests” for, much less go near, him for weeks or even months afterwards:

http://en.wikipedia.org/wiki/Less-lethal_weapon