One way to do ship-to-ship combat is to make the combat an encounter in of itself. Stat out the ship the characters are on as a regular monster (though probably with more HP, or a solo or something similar if the PCs only have a single ship), and the enemy ships as standard/elite monsters. Then give the PC ship special abilities depending on what kind of PCs you have, and allow the players to support the ship through their own abilities. For example, the ranger could make a precision shot against another ship's captain, dazing it for a while, or the wizard could conjure up a storm to either boost the PC ship or hinder enemy ships. There's no need to make the PC abilities literally what they have, as long as they work on a thematic basis. One or two at-will abilities and a couple of Recharge 4 abilities per PC should keep it interesting enough. If they want to board enemy ships you can bring the PCs out in their full stats (as well as perhaps supporting abilities from their ship).
If there are multiple ships, have each PC handle their own ship with unique abilities corresponding to their role. Defenders would have a Soldier-type ship, Strikers either Artillery or Skirmisher, Controllers have a Controller ship and Leaders have supporting abilities on top of the ship they'd be on (Warlords on a Soldier ship, Bards on a Controller, etc).
In addition, always have a secondary objective the characters need to accomplish instead of just "destroy all enemy ships".
Not sure it'd work perfectly, but at least it'd make an interesting diversion from the regular encounter paradigm.