Ferries and high-speed boats run from Tomari Port in Naha. The ferry takes about 70 minutes; the high-speed Marine Liner takes 35 minutes. Check the Tokashiki Village website for current schedules and fares.
It is also possible to charter a diving boat from Zamami or Aka island — roughly 8,000 yen from Aka and 10,000 yen from Zamami. These arrive at Aharen Port, not the main Tokashiki Port. Ask local dive shops on either island to arrange this.