You can just block the squito with nearly any shield, and counterattack if you can (a spear should be capable of being used on board a ship without damaging the vessel), though it may require keeping your health up to have enough block power to do so. But as others said, I'd also recommend training to shoot at them at range, it's very useful. And finally, sailing the longship is generally more safe all around, since they can take many more accidental hits.