the Disk Union chain is pretty good, they're a chain and have shops in many areas, with Shinjuku and Shibuya being the best, but all their shops are split into sub-shops so make sure to look out for the soul/funk/r'n'b ones.
Near the Disk Union in Shibuya there is a big building (opposite Tokyo Hands and just up the same road as Disk Union) which has about 5 record shops which sell a variety of soul/funk/r'n'b/reggae/ska plus in that general area there are quite a lot of soul record shops.