Imahan is one of the most famous Sukiyaki and Shabu-shabu restaurant around Tokyo. (However, I think Sukiyaki is more famous than Shabu-shabu)
They seem to have lunch shabu-shabu menu but not sure if they serve wagyu for lunch.
Seryna in Roppongi, another popular wagyu restaurant in Tokyo, serves wagyu Shabu-shabu lunch set for ¥4,320. Seems pretty affordable.
Rangetsu offers lunch Shabu-shabu, too but not sure if they serve wagyu beef.