DISCLAIMER: This might be common sense to some, but I don't think it was intended and might help some people out. I could not find any other posts detailing this method, so before you scream repost please find the original post! I'm sure this has been around since the dawn of the WoW, but I just discovered it while questing.
EXPLOIT: Another way to get inside a moving boat (or any moving object) is to swim in front of it, and wait for the boat to move into you. You will end up inside the bottom of the boat (most likely beneath the bottom floor inside the "crawl space"). Here you just need to swim and jump around like crazy until you pop up through the bottom floor of the boat. This should work the same with all other moving objects that are collidable, although water certainly makes this easier to pull off.
I used this trick in Howling Fjord to get inside a certain ship with a quest guy on board (I'm not sure how else to even get on the boat as its zooming around a lake and I didnt see any docks). This could also be useful as a way to sneak onto your other faction's boats without being noticed. I hope that some find this technique useful, and please post any other uses you can find in this thread.