Btw, Ninja's don't play by the rules. They don't sneak into your room, quitely wake you up and challenge you to a duel. They murder your whole family than disembowel you before hanging you by your own intestines, as ordered by their master.
People also seem to have forgotten ninjas have many ranged weapons, including poison spitting needle, shurikens and of course, bows, which are probably as effective as rifles/muskets/blunderbusses. You can fire an arrow every 5 seconds, but can't cap off more than 3 rounds a minute with a musket.
Finally, ninjas have magic armpits, which they can climb inside, and act as a portal. So a ninja can bridge the gap between land and the boat by climbing inside their magic armpits and appearing onboard, before climbing back out and tucking their armpits away. Translocation: Armpit Meditation is its official title.