That said, there are small places all over. this one might be relatively famous. It's next to a train track so not "quiet" but it's also in busy Tokyo.
https://maps.app.goo.gl/FMY9QwWyiibWn9CcA
Another thing there are lots of are small restaurants that hold 5-12 people. There are of course the famous bars in Golden Gai and a few other places but there really are 1000s of these places if you know where to look if you're language skills are up for it. Often there is person running the "bar" but they have a menu of food they'll cook for you. Things like grilled fish, pork salad, omelette rice, etc... Basically Japanese home cooking. Lots of people become regulars at a place and it's like their 2nd home.
If you watched Odd Taxi, they hang out at a place like this.
There's one I was introduced to recently right here (https://maps.app.goo.gl/Tgsfou4HMbKiiD3L8). It's not going to be around much longer because it's run by a 96yr old lady who lives there. She doesn't speak any English. She ran it with her husband until he passed away. IIRC she's been there 57yrs
Another, I was introduced to bar recently, not far from the coffee place above. I found it interesting in particular because it was only open weekdays from 5pm to 10:30 on weekdays. Not open on weekends. I haven't asked if that brings in enough or if the person has other sources of income. I'll ask next time I visit. But 5.5 hours a day, 5 days a week + prep sound nice.
Another thing I find appealing about these small bar/restaurants/snacks, they seem like not a bad life. Working a USA style sports bar in the USA or beer restaurant like in Germany or regular restaurant with 10+ tables seems like a not so interesting job. Just running from table to table taking orders, carrying orders, being "busy". These Japanese places are a place to socialize and in particular to socialize with the owner so the owner generally has a nice time as well.