I have to admit that when I asked "What do YOU want to know about Tokyo?" I wasn't expecting to receive a question about Islam & halal foods but that's just what CJCM from The Kuala Lumpur Traveler asked:
"Which Japanese city has the biggest Islamic community? Is finding halal foods a real big problem in cities such Tokyo?"
First, let's address the size of the Islamic Community in Japan. A read through The Shingetsu Institute of Japan article titled Islam in Japan taught me that in 2005 there were approximately 60,000 Muslims throughout the country and that only 10% are ethically Japanese. A large portion of the community hails from Indonesia and there are a dozen mosques listed in the article with contact information. Most of the mosques listed are in Tokyo but Kobe and Nagoya and a couple of other areas are also represented.
It appears that halal foods are not that difficult to come by in the Tokyo area. Tokoyfoodcast has reviewed four different stores and I found two others via an internet search. Baticrom and Spice Home both have online stores that service the Tokyo area. (I have not used these services and therefore cannot vouch for their reliability.)
I hope this helps you plan your next trip to Tokyo, CJCM!