All they gotta do is wait till the pirates pull up along side,, then pop up over the rail and fire 1/2 dozen flares into the little boat.  Then,, just pull away an let the pirates entertain themselves trying to put out their boat fire.

OR,, get a bunch of large heavy weights, etc.. when the little boat pulls along side, off load a few hundred pounds of weights, from the ship deck height to the boat anything weighing a 100 pounds or more would go right thru the deck and hull of those overgrown row boats.

Or,,,  A fire hose 4-6" hooked directly to a bilge pump would work, something that pumps 2000 gal a min would  fill those skiffs in 20-30 seconds an the pirates could play 'submarine'.... 

Or,, drape some old steel cables and wreck their prop.

Most ships have some sort of crane, forklift etc.. just dump a 1000 pounds of crap into those skiffs an, the pirates can play 'submarine'

Sounds dumb but even 50 gals of bunker oil dropped into the smal boats and a flare and have a BBQ !!

RPG's are tougher to defend against,, but plain old rifles and/or pistols don't mean krap IF the pirates can NOT actually board the ship.