At least since 9/11, the Coast Guard has been talking about Maritime Domain Awareness–the ability to keep track of everything approaching our coasts. The effort has used the Automatic Identification System (AIS) which gives the position and identification of cooperating vessels, and also anticipates cooperation with the Navy’s Maritime Patrol Aircraft and Broad Area Maritime Surveillance (BAMS) system which will use large land based unmanned aircraft, in addition to the Coast Guard’s own assets.
Concurrently the US has been developing a defense against ballistic missiles. (More info here on additional effort.) If they go to the trouble and expense of doing that, then they will almost certainly also develop a defense against cruise missiles as well, since it is relatively easy to launch cruise missiles against the US from nondescript container ships. The system that is likely to be used, the Army’s JLENS, has demonstrated a capability to track even small boats.
Sounds like the pieces of a comprehensive system that the Coast Guard may be able to exploit, may be coming together.