It is because st thomas and st croix are duty free. uscg now requires a cruising permit thats ia good for one year, meaning jan to dec. It dont cust much. Once you have it you can check in over thw phone on arrival.there is a station at the airport. I recomend you get the permit before hand.
It is impossible for the OP to get the permit for a boat he is chartering. Ideally the charter boat will already have the US Customs Decal Sticker on it https://help.cbp.gov/app/answers/list/kw/BOAT%20DECALS
If the boat does not have the sticker, they will just have to go in to the office and pay the $35 fee. Not a big deal either way. To clear in with just a phone call, the boat must have the sticker and all aboard must be US citizens. CBP can still request that all persons present themselves or have the boat inspected. That doesn't happen often but it does happen.