The famous review site TripAdvisor created a ranking of the top 30 restaurants in Japan chosen by travelers. Some of these restaurants can get very crowded, so if you can, making reservations in advance would be wise.
Guidebooks can be very useful, but also take a lot of time to read. Coming to Japan but not sure where to go? This list will give you the top 30 from a word-of-mouth by foreign tourists ranking on TripAdvisor.