There are many kinds of shops for geeks in Akihabara 秋葉原, Tokyo 東京.
These days, many tourists go shopping there which has caused the prices for many items (geek goods), especially second-hand toys, to become unreasonable.

Second-hand toy shops located outside of Akihabara are cheaper than the shops in Akihabara.
I recommend a second-hand toys chain Hobby OFF ホビーオフ.
If you are international tourists looking for Japanese toys for cheaper prices, you should take a look in the shops.

What kinds of items does Hobby OFF sell?
product category:
* Collectable Card
* Miniature Toy
* Girls Toy
* Boys Toy
* Gun, Military goods
* Radio control car
* Figure
* Plastic model
* Minicar
* Model railway
* Toys
* Video game (Retro game)

Website (in Japanese)

Their shops are usually located in the suburbs, and are not easy to access on foot, but 2 shops in Tokyo are near the stations.

Hobby OFF Kitasenju shop 北千住店
Google Maps
The nearest station is Kitasenju 北千住 Station
on Tokyo Metro 東京メトロ
on JR
on TSUKUBA EXPRESS つくばエクスプレス
on Tobu 東武

Hobby OFF Kameidotenjinmae shop 亀戸天神前店
Google Maps
The nearest stations are
Kameido 亀戸 Station on JR
Kameidosuijin 亀戸水神 Station on Tobu 東武

These shops business hours is 10:00am – 8:00pm, open every day.
You can walk to the shops for 7 – 10 minutes from the stations.