Sadly, gaming ain't what it used to be in Tokyo anymore, not that many worthwhile shops left.
Of course, check out Super Potato in Akihabara. Also be sure to go to The Mandarake and the retro Trader. They all have good stuff. I also recommend Nakano Broadway, it's a nerd mall with gaming stores and other weird shit.
Your mileage may vary, but I had a lot of fun going to arcades like Club Sega and Taito Station. There are some gaming and nerd stuff in Akihabara, although it is worth mentioning a lot of those stores have porn when you get pass the first floor. In my experience, I had better luck with that in Osaka. There’s a district called Nipponbashi that has more of what you would expect.
I don’t have too many recommendations for specific gaming stores. There’s a Super Potato in Akihabara, but I only went to the one in Nipponbashi. Shinjuku is a fun place in general, although it might be better if you have a general sense of what you’re going to do so you aren’t too lost.
I was there back in the summer and I would say I wasn't really trying to go shopping for games (especially seeing how easy it is to import now) but I was fully enamored by every Club Sega I passed by. I hadn't played any Taiko Drum Master before but I immediately saw the appeal. I also have a fondness for plushies that was sated during this trip.
Also, to be honest, if you're a SquareEnix fan at all the Final Fantasy cafe is actually pretty nice. I happened to be staying next to it during the last leg of my trip and figured it wouldn't be the worst thing I did, but the treats are good and I got another goddam plush (Baby King Behemoth) because of my affliction.
There are a ton of unique/weird games up higher in the arcades, if you're looking for something new and don't mind not being tutorial'd for some of it there are worse ways to spend your money. I never tried a pachinko parlor but boy do those places live up to the hype.
[Also, and this is entirely alcohol related, but if you are looking for a real amazing bar experience go to "Bar Benfidditch." It is incredibly hard to find (though it's on google maps) but probably the best drinks I have had in my life. It is the embodiment of style and class.]
I went earlier this year and just really liked looking at Japanese games and box art. All the stores others have recommended are great. The arcades are fun too, I saw plenty of people killing it on weird Japanese rhythm games. I even found a Theatrhythm machine that was fun to mess with, as a fan of the 3DS games :)