Another near Tokyo dive excursion would be Ito's Shark Scramble in Chiba prefecture. Akin to Mikomoto's Hammerheads, it is regular to see 200+ Banded Houndsharks, stingrays and other large fish here on a single dive. Cormorants also regularly dive in the waters in the winter. However the reason for there presence here is a bit unnatural, as they have been regularly fed here since 2009 in order to reduce bycatch in local fisheries in partnership with Ito Diving Service Bommie, who are also the only dive shop that operates in the area. Please make of that what you will.
The dive is up to 24m deep with potentially strong current so AOW is a must. Bommie also requires at divers to have at least 30 dives under their belt before reservation, though that is likely a non-issue for most AOW. Getting there is a bit tricky, as it is only a 2 hour drive to get there from central Tokyo, but as Chiba does not have the widespread rail lines of the Tokyo or Osaka areas, it takes around 4 hours to get there by public transport. This is about the same amount of time as taking the train to Shimoda or Minamizu, where boats to Mikomoto typically originate from, so if you don't have a car the two locations are almost equidistant.