It's a shame that your wife can't do the long haul/connection flights. Otherwise would have highly recommended Iriomote. You have to fly from Haneda, so that adds another 3 hours and then get the ferry from Ishigaki which takes about 45 minutes. The island is very jungle and fresh and beautiful. No franchises or even konbini stores. Great for snorkeling, nature and getting away from it all. Taipei is closer than Tokyo.
Runners up, imho, would be La Gomera, Formentera and (the more commercial but still full of non touristy places ) Sicily or Iceland.