Maybe you might have hear about those already but these are the shop I know aside from the brand ones.
Closet Child is a shop that sell 2nd hand (Visual Kei)CDs, and 2nd hand clothing form various Lolita or Gothic brands. (If you don't mind second hand that is...) Branches in Shinjuku, Harajuku, Ikebukuro and Yokohama(?) too. (
http://closetchild-cd.ocnk.net/)
There is Bodyline that sell mainly lolita cloth but got a fews gothic cloth once in awhile. I know 2 branches but there might be more. One is in Studio Alta at Shinjuku and another one is on the Takeshita Street in Harajuku. (
http://www.bodyline.co.jp/)
And there are some more shops that sell gothic and/or lolita clothing on Takeshita Street too.
Hope that was useful.^^
(geez, it's been ages since I posted here...@_@)