Are you concerned about the overfishing of the oceans, but still want to enjoy the delicious sweet raw flesh of fish? The Monterey Bay Aquarium has recently published a guide to what seafood you should and should not eat in specific areas of the United States. There is unfortunately no guide specific for Japan, but there is a US-centric sushi guide that may be of interest to some readers, and may encourage someone to create a version for Japan. (You’ll note that much of it is not useful because it depends on region — uni, for example, appears in all three categories, depending on its origin in the US).
You can download the pdf at the link.