The original Sushi Sho and many of their disciples restaurants (and restaurants operated by the disciples or sous chefs of the direct disciples of Sushi Sho), e.g. Sushi Sho Yotsuya (the first one), Sushi Murase, Takumi Shingo, Sushi Sho Saito, and probably others like Takumi Tatsuhiro, Sushi Iwase, Sushi Sho in Akita, Fudomae Iwasawa, Takumi Makoto, Takumi Owana and maybe some even lesser known ones. Sushi Sho / Nakazawa san was one of the first to do extended aging of tuna (upwards of 2 weeks) and buri, and him and his disciples (particularly the ones who follow the Sho school faithfully) are very well known for that. As far as other seafood, I’m not clear on how much aging is done, but certainly not everything is aged.
Sushi Kimura does not serve everything aged, for example: his anago or kuro awabi.
Quite a few other restaurants also age their fish but do not advertise it as they prefer to let the food speak for itself (e.g. Kurosaki). My guess it is a combination of light amount of aging (2 or 3 days) and perhaps counting the seafood’s handling conditions from the middle wholesalers and if seafood caught from further away from Tokyo, fish that have to be kept under rigid conditions for transport (mostly tuna from overseas but there could be others).
Other than the places you mentioned, Sushi Shinpaku in Ebisu serves aged fish as well for sushi. There’s also Jukusei Sushi Seimonten Yuga in Funabashi (Chiba Prefecture, about an hour east from Shinjuku by train).