Are there a lot of spellcasters with long-range abilities and/or access to things like cannons on board either ship?
If not, I would just ask the PCs what they want to do in game (ram the other ship, pull up alongside, attack from range, etc) and then assume they can do that since the other ship is nearly disabled. From there, you can have the intership fighting and/or negotiation.
remember, if a "flamethrower" like a wizard or sorcerer is around and reasonably common, then both ships will have access to countermeasures (smotherblend is an alchemical substance found in the Kenzer 3.5E book Salt & Sea Dogs: The Pirates of Tellene, which is a good source for combat at sea as well. Smotherblend will put out fires to prevent them from spreading)
If the PC ship is going to ram the other ship and the bad guys only have short range weapons, there is not much the bad guys can do to prevent the ramming, as the PC's ship will have momentum going forward and most low to mid level damage outputs won't sink/stop the ship in time once its in short range.