Found this. Basically they can do what ever they want.
http://www.rcmp-grc.gc.ca/ibet-eipf/shiprider-eng.htm#shiprider
This is how the USCG see's things.
Sorry, but when it comes to Coast Guard boardings, you don’t have any rights.
I’m surprised how many boaters don’t know this. The US Coast Guard can board your boat any time they want, and look anywhere they want, without probable cause or a warrant. They can do this on the open sea, or while you’re asleep aboard in your marina at midnight. They can look through your bedsheets, in your lockers, in your bilges, in your jewelry box, or in your pockets. They can do it carrying just their side arms, or they can do it carrying assault rifles. They can be polite about it or they can be rude, but mostly they’re polite.
The U.S. Coast Guard Boarding Policy:
Title 14 section 89 of the United States Code authorizes the U.S. Coast Guard to board vessels subject to the jurisdiction of the United States, anytime, any place upon the high seas and upon any waterway over which the United States has jurisdiction, to make inquires, examinations, inspections, searches, seizures, and arrests. The U.S. Coast Guard does
not require a warrant to conduct search, seizures, arrests over any United States Waterway or high seas. The U.S. Coast Guard also have full legal law enforcement power on any land under the control of the United States, as needed to complete any mission.
They have sweeping powers. “In terms of enforcement power, Coast Guard boarding officers are clearly America's supercops. As such, these provisions comprise what has been accurately characterized as 'one of the most sweeping grants of police authority ever to be written into U.S. law.
Here’s
an article by a retired Coast Guard captain and Coast Guard legal counsel. The pull quote kind of says it all: “There are two main ways to board a vessel—either with permission, or without.”