Disney normally docks at Havensite. I assume you are asking about the ferry to St. John. You can either get one at Red Hook (opposite side of the island requiring a taxi ride over the mountains) or one at the waterfront in Charlotte Amalie (longer boat ride).
Red Hook is not far, maybe 9 or 10 miles, but you want to give yourself about 1/2 hour each way. Unfortunately, the ferry times from Charlotte Amalie are not really conducive to a day trip to St. John when arriving by cruise ship.
We hopped in a taxi and were there in 15 minutes or so. The Ferry was on time (!) both ways (to and from St. John) and had lots of seating inside and topside in the air. The transit was around 10 minutes.
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