Scott J.
Google
Disk Union is the best record store I've visited anywhere in the world. Deep selection, fair pricing, and friendly staff. It took me 3-4 hours to dig through all of their locations in Shinjuku; it was a fun afternoon!
Some details to keep in mind: Each floor of each of their locations is basically its own record store; you check out separately before moving to the next floor, and while each floor is largely dedicated to a genre, they each have general sections and small sections devoted to other genres (e.g. Soul sections in the various Rock floors), so make sure to take time to visit them all.