like the others have mentioned, there is no actual ZoZotown. However, you will find most of the shops listed under the ZoZotown website to have branches in Tokyo's Shibuya, Harajuku, Ikebukuro districts.
The key brands shown in Zozotown are United Arrows, Beams, etc... If these are the brands you're looking for, you will definitely find them in all 3 of the districts I've listed above, as well as in Shinjuku. For Porter bags, you'll also find them in Tokyu Hands -- the Porter/Kurachika shop in Harajuku is not easy to find, and the hours they open are kind of strange, so I suggest you go to Tokyu Hands (either in Shibuya, or Ikebukuro).