As a Merchant sailor, I have a LOT of experience in this area...
If you are only going to be pulling into the exact same port repeatedly, then you may carry weapons on board that are allowed by the port you are in. Many ports will not allow weapons through the gate, which is why many Merchant vessels are being taken over without opposition. Many host countries will not let vessels dock at their ports if they have even a single weapon on board, but some will allow minor small arms, such as shotguns.
My company has recently invested in the LRAD (Long range acoustic device) which has been shown to work as a deterrant, but if a pirate really wants to get your ship, they will just come back wearing really good hearing protection and thick clothing to combat the LRAD.
Most of the pirates operating in the "hot zone" (Off somalia and india) are armed with AK47's, RPGs, and various other small arms, some boats even having 50BMG machine guns mounted.
If a pirate cannot take a vessel, they have been known to just blow it up with the RPG's, or at least blow part of it off.
I doubt you're fishing in the "hot zone" so I don't think you have *too* much to worry about, but if you want the best protection available, grab an LRAD, grab a few shotguns, and a few semiauto rifles, as well as a few pistols for your crew.
You wouldn't know that a closing vessel is a pirate until they are in small arms range anyway. Most vessels don't know a pirate is coming until they're actually along side attempting to board.
Just my .02 on the subject