I present our slowly expanding list of gluten free and low gluten restaurant options around Tokyo and Kanagawa! Some of the restaurants don't claim to be gluten free (other than the noodles) so it's probably best to consider these as low gluten options, as long as you stick to salt (shio) bases.
Shibuya-ku. All gluten free - very generously sized pizzas and sandwiches. Haven't tried the ramen yet but it looks nice too!
Shin-Yokohama. A ramen restaurant inside the Shin-Yokohama ramen museum (worth a visit!) which has a gluten-free noodle option.
Tokyo station, Kyobashi, and Hirakawacho. Terrific ramen restaurant with a brown rice noodle option. They have vegetarian and vegan options which contain barley, but apparently it's possible to ask for them without this.
Various locations. Another great ramen restaurant with a gluten free konnyaku noodle option.
Minato-ku. Gluten free pizza bases are available.
Kamakura. Bento, pizza toast, curry, burger, and sweets, all gluten free and made with rice flour.
Shinjuku-ku. Gluten free specialty cafe - on our list to check out!
Harajuku, Yokohama, and Kamakura. Hawaiian style burgers with gluten free rice flour and 'vegetable' bun options.