I like small shops also!
Kawagoe and Yanesen are beautiful places. Tateishi is more deep spot.
If you like small Izakaya restaurants (like a pub), my recommendations are Nakano and Asakusa hoppy street. The area has "Yokocho". Yokocho has many mom-and-pop Izakaya restaurants.
Un...If you dont like Izakaya style...
Some Tokyo's area has famous and bigger shopping streets.
The shopping street has many mom-and-pop shops.
1. Sugamo Jizo shopping street
2. Togoshi-Ginza shopping street
3. Asakusa Nakamise shopping street ( famous travel spots )
4. Nakano Sun Mall shopping street ( famous for subcultures )
If you are interested, please try searching.
Yokocho and Shopping street are may be good keywords for you to research.