Depends on which ships. But always get a galleon and good gear. Get gear from the bazaar and save up gold for that galleon. I find the only reason I get through skyways are galleons (plus they look cool and have a bunch of cannons,( pirate little red riding hood, little red sailing hood, grandma, why do you have so many cannons on your ship, wolf, the better to blast you with my dear )
Keep pressing 1,2,3,4 on your keyboard until you sink an enemy ship.
Seriously, in order to survive at least one ship encounter, you must keep your nautical level and your ship up to par with each new skyway. You can also bring a friend or three to help defeat ships faster.