Overseas clearance to enter CZ/TTW/Major Harbors?

Former USN SWO here, doing some research for a grad school project. I was wondering what the procedures are for requesting/granting clearance into US harbors (or EEZ/CG/TW, wherever you draw the line) for smaller vessels coming from overseas. For instance, do you screen all vessels entering Verrazano or the Golden Gate? Happy to provide more details, shoot me a PM.