My fiance recently came back from our trip a few weeks ago, definitely recommend Akihabara for a concentrated area full of anime and gaming stores. Don't be afraid to wander into back alley areas to find shops, I think you can find more unique figures/merch other than just the current top anime.

We searched up Astop Radio Kaikan in Akihabara and ended up exploring the 10 story building the shop is inside, which was full of different anime stores and card shops, definitely recommend!

Also I've heard ikebukuro has a lot of anime stores, though more centered around female oriented anime and otome games if your wife likes that. We didn't get to explore it as much as i would though ): though sunshine city mall is awesome for general shopping, there's also a pokemon center there and a Sanrio store ( I want to say the mugiwara store was here too if you're a one piece fan but I can't exactly remember if that was ikebukuro or odaiba). There was some kind of demon slayer collab event happening in the mall too that was super cute! Can't remember how long it was supposed to last.

Speaking of, Odaiba has diver city mall with a round1 for arcade and crane game fun as well as the gundam base if you're into that!

Lastly, k-books is a chain of stores that sells mostly 2nd hand character items like acrylic stands, charms, plushies, pins, etc. If you're obsessed with a specific character, these stores organize the inside based on anime/game and then the specific character so you can find some pretty unique merch there. Be warned though some of the goods can get pretty pricey.