Charlotte Amalie is compact and walkable if you are reasonably fit — the historic district is mostly flat along the waterfront, though the hillside neighbourhoods above involve real climbing. The 99 Steps and other stairways cut directly up the slope and are the fastest route on foot.
Taxis are plentiful, operate on fixed zone rates, and are the standard way to get around for anything beyond walking distance. The main taxi stand is near the cruise pier. Note that in the US Virgin Islands, driving is on the left, despite American cars and road signs — a Danish legacy that catches many visitors off guard.
Buses (called "safaris" locally — open-sided truck conversions) run along the main roads of St. Thomas and are cheap. They are useful for getting to the island's beaches and other parts of St. Thomas, though they require some local knowledge to navigate.
The ferry to neighbouring St. John departs from the Red Hook ferry terminal on the east end of the island, or from the downtown ferry dock near the cruise terminal — the latter service takes longer but is more convenient from Charlotte Amalie.