There is no customs in St John. The building was destroyed. Right now all of the Ferry's are coming to St Thomas to the main ferry terminal. All of them except for Inter Island Boat Services offload there. Where you will have to take a cab to Red Hook and then take the St John Ferry Back. Interisland runs from Red Hook so if you can make their schedule you can ride the Ferry back to Red Hook and then take the St John Ferry.
They are supposed to be opening a Customs Office in Red Hook. A sign that I saw last week at the Red Hook Ferry terminal made it look like that would happen by April 9th. So this could change before your trip.
