For stores, Dynamic Audio in Akihabara has something like 6 floors with prices increasing as you move up each floor. The top floor (7th or 8th, can't remember) is pretty awesome. You can just walk in and listen if there's no other customers demoing equipment.
For accessories, Yodobashi camera, also in Akihabara, is pretty awesome.
I've visited both Shindo and Kondo, and both visits were fantastic. But you'll likely need to speak Japanese to set up the visit.
If you spin vinyl, record stores in Tokyo are pretty awesome, but they seem to be more picked over these days. You'll still be able to find some nice stuff at reasonable prices though.