Allow me to recommend this thread: IC Guide to Game Shoppin in Tokyo
City Shrouded in Shadow will be slightly frustrating to find as it is not pricey enough to be in the showcase, so you’ll need to look for it on the shelves. Find a picture of the spine that you can pull up on your phone when browsing so you can recognise the kanji.
Pokemon games are everywhere and I imagine Mother 3 will be as well.
My recommendation for if you just want to get those three and not spend too much time browsing, is to go to Akihabara and hit up Super Potato and Surugaya. You will pay the highest prices there, but I’d be amazed if you don’t come away with all of them from one trip.
If you want to do some more hunting to get better prices, the Surugaya in Shinjuku is good and has become my go to. I also recommend the Mandarake game store in Nakano Broadway (4 minute train ride from Shinjuku). Nakano Broadway is full of cool shops and looks like a SMT dungeon. The stair layout is crazy and it can be tough to find. I think it is on the second floor. Go in the afternoon as a lot of stores don’t open in the morning.
If you have the time and you’re going on day trips, look in Hard Offs outside the main cities for bargains. Book Offs are everywhere in Tokyo and often contain treasure.
For new release stuff, your best bet are any Book Offs, but especially the one opposite the Shinjuku Station West Exit. It is above a suit shop and is rammed with PS4/PS5 and Switch. If you want it to be brand new, go to Yodobashi Camera.
BTW, are you looking for foreigner friendly restaurant advice? I went to Tokyo earlier in the year by myself and can help with that after some good experiences I had.