Yes, Ochanomizu is great.
There's a whole road of guitar shops just outside the station.
I can't recommend just one, but if you can't find what you need along that street, I'd be very surprised.
I sometimes go to Kichijoji. Kichijoji is closer for me, and I bought an amp from there.
It was easier to get it back home.
They have two good guitar shops. One big, one small.
I found the link to the one closest to the station.
http://www.rockinn.co.jp/shoplist/kichijoji.html
I think the other is Yamano Music...can't remember to be exact, but it's bigger and has a good selection of vintage guitars.