Some things to spice up combat on a ship. (tech may be too low in a few examples)
1- Sharpshooters. A common tactic was the placement of sharpshooters up the masts. These make nice targets for your PCs, as they're somewhat distinct from "average guy engaging in melee."
2- Sail Cutters. If ballistae are used, a large ship is capable of putting spiked/razor sharp chains on at the center of gravity of two ballista bolts. While typically they can be used at medium range to slow ship by slashing through the sails, no one would think twice of sending one through a massed group of combatants on board. Be as descriptive as you like in detailing what razor sharp chain does to a cluster of lightly armored seamen when traveling at 70 odd miles an hour. Heads may roll, Torsos may thump, or the peg-leg guy at the harbor may be in for a lot of business ^_^
3- Lit Arrows. Are some of your PCs not combat oriented, no doubt a few lack HP. Putting out arrows is an excellent task for people who don't want to be absolutely useless but don't want to impale themselves on a saber.
4- Fire Ships. If a ship just won't surrender, but has too many combatants on board and cargo isn't the point of the raid, there's nothing wrong with putting explosives on rowboats, putting a few stout lads on it, and sending them to do some dirty work. Just get the boat stuck to the ship (Rudder? Yeah) and light a few fuses, then dive and escape. Cannons etc usually have a hell of a time hitting these little buggers when they get close, and if nothing else it'll give your PCs yet-another-problem to deal with.
5- Ramming. If your boats support bronze or steel rams, you can always have the final attack of the opponents be a ram of some sort. This defies Age of Discovery tactics (lets line up and broadside each other repeatedly fighting for the best winds) but, hey... could happen. Anyway, handling a crew is one problem, handling a captain bent on smashing into you full speed is a total other problem. It'll make the PCs figure a way to get onto the boat, kill the big Bad, and win the day.. Or, it'll make the cast deal with now owning a completely different ship if they fail to stop the ram but win the day.