Nakano

Nakano isn't that worth visiting, but there's a store in the shotengai (shopping street) there that has some good indiepop bargains.

Fujiya Avic

It will be hard to find this place. Go out the north exit and walk into the shotengai. You'll pass a McDonald's on the left. Keep walking until you're not in just a street with a cover over it, but you're actually in a building. It's in that building, on the third floor.

Nakano Broadway
Nakano 5-52-15
Nakano-ku, Tokyo
http://www.fujiya-avic.co.jp

Other Places

You will also find plenty of record stores in Kichijoji. It's a good place to explore casually anyway if you have time.

In Kamakura, I happened into this place Casino Classics that was great:

Stroll Building 2F
Shomachi (I could be pronouncing this wrong) 2-10-7
Kamakura-shi
248-0006
0467-25-1035