There is a recent 3 part article on Coast Guard boardings and your Fourth Amendment rights from sailfeed.com. It is very informative, as well as links to other writings on the subject.
If you wish to skip the reading, I will summarize it for you:
You don't have any Fourth Amendment rights on the water, and haven't since 1790.
“There are two main ways to board a vessel—either with permission, or without.”
Had to delete link. Only had 9 posts and I need 10. See if I can post it next...