In Red Hook, the captain will meet you outside gate C at American Yacht Harbor (AYH). A taxi can drop you off right there.
If you drive, you have a couple options. If there is room in the AYH garage, you can park there, but make sure you go to the marina office and ask to pay for a day pass to put in your windshield (They are serious about booting you past 2 hours during the day). You could also park behind Moe's Fresh Market (across the street and up the hill) or at the ferry garage (possibly the cheapest option).
If you get confused, lost, or are unsure of what to do, call Captain Ryan at 443-831-1911. He'll be happy to help you out!