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Somewhere no one seems to expect is Yamashiroya right across (south) from the Ueno station
I found a Jojo's SHS Kira figure there unopened for 3000!
They've got all kinds of figma ranging from standard to the more rare finds (Black Knight Guts Kreygasm) and a huge selection of old-school models including gunpla and gaogaigar type bandai kits.
Also, if you're the bar-going type stop in The World End and if you meet a bartender named Yuta tell him Jesse the bearded one sent you, kinda became a frequent customer over the 5 weeks I was staying in Ueno this year.