We've cleared in several places in the Caribbean, but mostly in the Virgin Islands. There are definitely different practices between the BVI and USVI. In the BVI the captain goes in alone with ships papers and forms filled out and signed by everyone aboard (including kids) along with passports.
Checking into the USVI, everyone must appear in person.
Something to keep in mind: The importation of fruits and vegetables is an issue, certainly in the USVI. Don't try to bring a Florida orange that you purchased in the BVI, back into the US!