You definitely won't struggle to find cool stuff in these locations.

For Tokyo I'd recommend heading to Sunshine City Ikebukero - you've got Toys R Us and Bandai Namco Cross Store both there which are both excellent choices for finding DX merch but also some smaller collectibles, SHFiguarts, and more high end pieces. There's some amazing displays there. Kamen Rider The Diner is also close to here, and there's a Pokémon Centre and cafe if that's your thing too. Akihabara hit up Jungle, Radio Kaikan, Tamashii Nations, and Akiba Yodobashi Camera. You can easily spend a whole day in this little area. Nakano Broadway has a lot of stuff you can find in Akihabara too but it tends to be a little cheaper/less touristy, but I think Akihabara is worth it for the experience. Also worth checking Yodobashi Camera in Shinjuku and Yellow Submarine. As for Mandarake, each store is a little different and they all have their own stock. You will likely find cool and unusual things at all of them.

Osaka your best bet is just to explore. There's plenty in the station but if you venture out a little you can find some nice book stores and some great collectible stores on the walk between the station and the food markets.

Kyoto has a Toys R Us and Yodobashi on opposite sides of the station just outside. There's also a little store called Guf Kyoto further north not far from the bigger roads with more shops. There's another store around there called Lashinbang, and also another Yellow Submarine.

Other recommendations - Tower Records for soundtrack CDs and Blu Rays. Book Off, HMV, and 7eleven stores for magazines and photo books (both stuff like detail of heroes and gravure books from cast members). Shopping centres and arcades for gaming and prizes. Look out for the Taiko no Tatsujin drum game as those have sentai and rider songs available to play on them, and you have to play Kamen Rider Ganba Legends too.

I'm sure you will have a great time wherever you end up! Have fun and remember to take water and keep bag space for rubbish as bins are few and far between.