You can find Volks dolls in their shops all over Tokyo. Also they have stores in different cities (Kyoto, Nagoya, Hiroshima, Osaka etc).
Volks have created dollfies and super dollfies, they are first and one of the most prestigeous companies.
Their dolls are very expensive (depending on the size, wether it is limited or standard edition, one off, etc).
VOLKS INC. - Online Shopping, Doll Hobby, Grage-kit, Figure, Robot & more
Second hand dolls are available in stores like Mandrake, in Akihabara and Nagano.
Korean company Soom, also have store in Tokyo.
http://dollsoom.com/soom/
Cheaper dolls are chinese ones and they are not usually available within Japan.
edit: basically there are no other japanese companies selling dollfie/super dollfies than Volks (they have monopoly on dollfies in Japan)