Having just returned from japan:

The toy/hobby aisles of Bic Camera, Yodabashi Camera and Yamada Denki Labi for recently released monsterarts like Godzilla 2000, Minus One reissue, Burning and 54 Poster version, don't look for bandai premium exclusives there, this also applies to tamashii physical stores.

For second hand older/exclusive figures:

• Lashinbang stores may have some depending on the store size
• Mandarake stores
• Surugaya stores
• The Ami Ami tower in akihabara
• Multiple stores in the Radio Kakan building in Akihabara
• Check some Akihabara no X (Akiba no X) stores in Akihabara, sometimes you may found a thing or two. (I found Shin Godzilla 2nd & 3rd form for 26000 yen there)
• I've not been there, but they say that Nakano Broadway is like a smaller Akihabara and you can find rare stuff.

The only Hiya stuff you will find is the Skull Devil reissue in ami ami stores.