I sailed out of Red Hook on a charter/sail course a couple of years ago.

Given your late arrival, getting picked up at Red Hook is the better option IMHO. Especially, if it is only an extra $300.

If it is your first trip and you are arriving that late you will be apprehensive and anxious as to whether you will make the ferry either out of CA or over to Red hook. Then, as other posters stated, you have to get through customs and taxi to wherever the boat will be. By this point it will be close to dark and you won't be going anywhere most likely. stressed, tired. What's the point?

The alternative is have them meet you in Red hook, as you originally suggested. If you get in to CA on time, you would have enough time to sail over to Christmas cove, Cruz bay or Francis Bay on St John. Enjoying a wonderful evening under the stars on the hook your first night sounds like a pretty good start!

Worst comes to worst and you are late arriving you can still meet the boat in Red hook and stay the night on a slip. The boat will be waiting for you! Red hook is a nice little port with lots of restaurants, bars and souvenir shops to explore your first night. Not a bad worst case scenario!

The next morning you can sail into Soper's Hole and clear in or Jost depending on your itinerary.