It is a decision with options. Since the OP didn't say whether they were clearing in on STJ or on STT or intending not to clear in at all, it's hard to give them suggestions. They also didn't indicate if they want to dump passengers and dash back to the BVI or spend time here. Sail2wind provided a decent option.

As to clearing in at Cruz Bay, C&I has been fine with people coming straight from the BVI to St Thomas and clearing in at either Yacht Haven or by the seaplane. I know that's not exactly how the regs read...