Thanks for the replies!

Changing where we charter is not an option at this point. Our charter and dates are fixed, which limits our flight options considerably.

It's just my girlfriend and I flying. Our charter group is four total, but our arrivals and departures are staggered.

Jason, thank you for your detailed insight. If we fly to EIS will we only have to clear customs once? My understanding is that flying to STT we would have to clear customs there, and again in the BVI. I'm not too worried about the entry as we have plenty of time. Our first night is a sleep aboard on the boat. I am worried about the exit with the testing requirements. I'd like to simplify that as much as possible.

Right now the itinerary I'm liking the most looks like this:

Outbound:
17:48 Vancouver > 18:50 Seattle
2h 55m wait
19:45 Seattle > 06:00 1Newark (next day)
2h 20m wait
08:20 Newark > 13:23 San Juan
2h 52m wait
16:15 San Juan > 17:00 Beef Island

Return:
12:00 Beef Island > 12:45 San Juan
3h 15m wait
16:00 San Juan > 19:50 Toronto
2h 30m wait
22:20 Toronto > 00:38 Vancouver

Scratch that. I made the mistake of leaving the number of travers set to one. It appears that itinerary is not available for two.

When looking at flights for 2 it appears there is a much better option into STT… How much more horrible is it, really, to come in through STT and have to deal with the ferries. We will only have one small backpack each. Are there any gotchas I might not be aware of?