If it were my boat that was in charter service, I'd want the charter company to tell you to stay outside at a mooring and dingy in.
The most challenging moment in Cruz Bay for us was getting off the Customs dock with ferry traffic and several excursion boats circling as they awaited our departure. The Customs folks had shoehorned us in to the point of our bow overhanging the transom of the boat ahead of us and our transom nearly touching the bow of the excursion boat that came in right after us. If we didn't have a bow thruster on the IP 420, I would have deployed the dinghy as a tow boat to pull the bow off the dock! Once off the dock, we had to make a sharp U-turn and thread our way through the heavy traffic--several excursion catamarans-- but that was the easy part, once we had way on. For some reason, we had arrived at the beginning of rush hour. Had we arrived 15 minutes later, we never would have been able to tie up at the customs dock. To OvO's comment, I'd say the issue is BOTH docking and traffic, unless you come in at a quiet time.
I've been sailing in the USVI / BVI since 1978, yet despite all that experience, your description above reinforces my perception that taking a bareboat into Cruz Bay is not a good idea.
It would be easier to sail to JVD, check-in and get water in Great Harbor. Now I just need to decide if it's worth the extra cost to charter the 440 (more space for family of 5, more water, two heads). With either IYC boat it will be a good experience, of that I'm certain.