The restaurant is located on Ramen Street, on the B1 floor of Tokyo station near the Yaesu south exit. Just look (or ask) for Ramen Street and you will find it.
at the entrance, where they also have menus in English and pictures to explain what each soup contains. I asked if it was possible to get the standard, soy sauce based, with rice noodles and the staff assured me that I could get it gluten-free. They asked if I was allergic and said it would take some extra time as they would prepare my food separately. So make sure you tell the staff that you can't eat gluten and that you want your meal gluten-free.
In Japan wheat allergy is more common and most people think that I'm allergic to wheat, which is not the case, but since wheat is the most commonly used grain here I usually get by with asking if the food contains wheat or wheat flour.
小麦 komugi (wheat) and 小麦粉 komugiko (wheat flour) are good vocabulary to learn. I personally can eat soy sauce, but if you can't then the soy sauce based one is not a choice of course. The vegetarian gluten-free ramen is really worth trying, it is super tasty and since the broth is thick and full of vegetables you won't leave Sora no Iro still feeling hungry! I also enjoyed trying the more traditional ramen with soy sauce based broth (not vegan or vegetarian) with gluten-free noodles since it is such a rare, well almost impossible, treat to get gluten-free ramen in Japan. It is not as filling as the vegetable filled one, but still very satisfying. You can also enjoy some other small dishes and toppings, vegan soy milk ice cream and craft beer. The price is a bit on the more expensive side, with the standard vegan and vegetarian noodle soups starting at ¥900. The gluten-free brown rice noodles will set you back an additional ¥150, but I think it's definitely worth it!
There is a third restaurant, the Kyobashi shop Soranoiro - Tokotsu and Kinoko but from what I know they don't serve vegetarian, vegan or gluten-free noodle soup. Their focus is on tonkotsu (pork bone broth) and kinoko (Japanese mushrooms).