Japanese games are world famous, but older games are not sold much in Japan.
However, there are shops dealing in Akihabara in Tokyo.
There are several shops selling NES(Nintendo) , SNES(Super Nintendo) , Game Boy, Nintendo 64, disk system, NEOGEO, PC engine, Mega Drive, Saturn, Dreamcast, PlayStation, etc. … in Akihabara.
1, Retro Game CAMP
ADRESS：Kowa Denki Bld., 4-4-2, Sotokanda, Chiyoda-ku, Tokyo
OPEN：11:00-20:00
Open throughout the year
2,BEEP AKIHABARA
ADRESS：B1F, Nakae Bld., 3-9-8, Sotokanda, Chiyoda-ku, Tokyo
OPEN：11:00-20:00
Regular holiday：Wednesday, Thursday
3,SURUGAYA AKIHABARA GAME
ADRESS：1F, Toyo Bld., 3-9-8, Sotokanda, Chiyoda-ku, Tokyo
OPEN：11:00-22:00
Open throughout the year
4,TRADER
ADRESS：Trader Bld., 3-14-10, Sotokanda, Chiyoda-ku, Tokyo
OPEN：11:00-20:00
Open throughout the year
5,SUPER POTATO
ADRESS：Kitabayasi Bld.3.4.5F, 1-11-2, Sotokanda, Chiyoda-ku, Tokyo
OPEN：11:00-20:00
Open throughout the year
There are still small shops in addition to this.
Please try searching while taking a walk in Akihabara.