I am not 100% positive and others may have more recent experience, but I think that if you have to file an I-94 to enter the US, that you cannot use CPB Roam. See https://www.cbp.gov/travel/pleasure-boats-private-flyers/pleasure-boat-overview/roam. If this is correct, my guess is that you will have to go to the Customs/Immigration office at the airport on Culebra. I think there is also one on Vieques at the airport there.

The last time we went, CPB was not in effect and we had to call Customs from the anchorage in Ensenada Honda. We provided the boat registration, names and passport information and were given the ok in about 10 minutes. We were all US Citizens. Regardless, the Customs Officer had the righ to request that everyone present themselves in person.