I got my Japanese visa stamp in Naha, Okinawa. I flew from Taipei, Taiwan, with flypeach com. The airline has not got too many favourable reviews, but speaking from my own experience I was satisfied with the service. The flight was on time and comfy for a budget airline. The most negative opinion it receives is that the planes touch down in the cargo area and you have to take a connecting bus to the main terminal, which is free anyway.
More official info:
Any foreign visitor who wishes to enter Japan must have a passport, which will remain valid during the period of stay. In order to enter Japan, visitors usually must comply with the conditions of their visas and authorizations of resident eligibility. However, visa exemptions can be made for citizens of sixty-six different countries provided that their stays are within ninety days such as with stays for sightseeing purposes and that they do not engage in activities where they earn compensation. This page provides information on short stays. Revisions in visa conditions are made periodically. Therefore, please check the “Visa” section in the Ministry of Foreign Affairs of Japan website if the latest and detailed information on standard visas or visas other than for those for short stay programs is needed.