The direct answer: Akihabara in Tokyo has the widest selection and is the easiest to reach, but it's also the most crowded and touristy. If you want the same shops (Mandarake, figure stores, retro games) with a fraction of the people, go to Den Den Town in Osaka or Nakano Broadway instead — both sell to locals first, tourists second.
What to Buy, Where
Figures & scale statues
Kotobukiya, AmiAmi physical stores, Mandarake for used/rare
Manga & light novels (used, cheap)
Mandarake, BOOKOFF — often ¥100–300 per volume
Retro & used video games
Super Potato (Akihabara), Mandarake, Den Den Town shops
Gacha / capsule toys
Literally everywhere — bring ¥100 and ¥500 coins, machines don't take cards
Studio Ghibli goods
Donguri Kyowakoku (multiple locations) — no ticket required, unlike the Ghibli Museum itself
Pokémon specifically
Pokémon Center Mega Tokyo (Ikebukuro) or Pokémon Center Shibuya
Nintendo specifically
Nintendo TOKYO, inside Shibuya PARCO
Before You Go
Tax-free shopping: bring your passport — most stores need a minimum ¥5,000 purchase (before tax) to waive the 10% consumption tax, done at the register on the spot.
Gacha machines are cash-only: keep a stack of ¥100 and ¥500 coins on hand. Convenience stores nearby can break bigger bills.
Mandarake grades used goods by condition (often marked A/B/C on the price tag) — check for this before assuming a low price means low quality.
Most shops stay open late (until 8–10pm), which makes this a good after-dinner activity rather than a full separate day.
Large or fragile figures: consider shipping home from the store if available, or pack them in carry-on — checked luggage is rougher on boxed figures than it looks.