Technically, the US military is not suppose
to act on US Soil (at least not in the states, I
don't really know about territories).

In fact, whenever a US Naval Vessel makes a stop,
a US Coast Guard Offuce MUST be present to take
law enforcement action.

The Patriot Act does not change that.
However, it certainly provides much greater leeway
by "Law Enforcement Agencies".
NSA is technically part of the Dept. of Defense.
It has been pushed over to the:
- FBI
- Coast Guard
- Dept. of Homeland Security
in order to avoid the "military involvement" issues on
homeland soil within our borders.

There are actually several "borders" defined on the seas.
12-mile statue is the one that comes to mind relating
to that involvement.
Some of the other broders relate to "Economic Involvement" or
impact, etc.