Nissin World Delicatessen in Azabu-Juban where I buy most of my meat. They have a lot of halal meat, but it's all imported. I often buy NZ tenderloin that is halal. I have even seen a whole lamb in the freezer section. But the Wagyu is not halal.
http://www.nissinham.co.jp/nwd/

p.s. Regarding the link from Kyushuguy, purchasing a block of 2 kilo Wagyu for 20,000 yen is pretty good value. The basic domestic (prefecture not specified) black Wagyu (黒和牛）fillet sold in the supermarket is about 900something yen for 100 g. It's sold in annoyingly small pieces. The most expensive Wagyu goes for about 4000/ 100 g. At Nissin they have Wagyu tenderloin for 1500 and another type for closer to 3000.