I can’t remember specific stores but in the Akihabara area I think lots of places carry models. I vaguely remember seeing some in the department stores, the mindblowingly large and diverse department stores around Shinjuku station.
Directly across from the American Yokota Air Base there is a hobby store but the airliner selection wasn’t massive and it’s probably 45 min to an hour train ride west of the city. The models I saw in Tokyo were not unique or less expensive than what I’ve seen online so I didn’t buy anything. It would be the home to 1/200 ANA/JAL models though 
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