I second Book Off/Hard Off. From everything I've researched (and I've been doing this for about three years now...it's a life long goal of mine to go to Japan), those two stores are easily the best place for cheap games. Akihabara you go for the experience, not to game hunt. It's a tourist trap and the prices reflect that. It's an amazing place and you should totally go, just don't spend money on buying games...spend it in maid cafes or arcades. However if rare is what you're after...Akihabara is the best place for super rare stuff. Just know you'll pay an arm and a leg for it.
I recommend checking out this channel, he lives in Japan and often game hunts in Book Off/Hard Offs and it'll give you an idea of prices and what you can expect to find:
https://www.youtube.com/user/KidS...
If you go to those stores, dig through the junk bins! Often games are labeled as "junk" if the condition is off or they happen to have to many copies of the game (think Final Fantasy and Dragon Quest stuff). And when I say the condition is off? I mean it's near mint...lol. The Japanese are amazing with their condition of items. They mark the prices down accordingly if something is wrong. Watch the channel I linked to, to see. You can really get an idea of the condition Japanese games are kept in. I mean sure there will be some yellowed cartridges or the odd one where someone wrote their name on it but from what I've seen in his videos, 80% of games look perfect.