When I was in Akihabara six months ago, I found these arcade shops. One is called
Try Tower. A very small shop which is more a front to a warehouse than a shop. They had some showcases with joysticks and parts though. Try Tower also has a multi-story arcade in Akihabara with the top floors having only retro games like Gradius, Wonder Boy in Monster Land, Super Mario Bros, Darius, etc.
Another, much larger shop with plenty of items on display is
G-Front. I recommend this shop for browsing. You never know what you might find.
In both shops I had trouble getting the staff to help me. Despite studying Japanese for two years they didn't bother to tolerate this
gaijin's imperfect Japanese utterings. None of the staff spoke any English beside "Sorry, no stock". If you are not fluent in Japanese I recommend getting a native speaker to translate for you.
A quick search on Google also turned up this shop,
Mak Japan, in Akihabara. Not been there myself, but can't hurt to check it out.
Hope this helps you a bit.