A few doors down from the coin laundry I use, on a side street next to the local Dominos Pizza delivery center, is Juniso.
This could be a possible contender for a consistent late-night bowl; if they were only open late.
Everything was solid, nothing stood out. The atmosphere was that of your average just-off-the-main-road ramen shop in Japan.
It is a funky spot, Nishi-Shinjuku-4-Chome. Technically, it is the closest residential hood to the famous skyscraper district (unless you count the massive homeless population in nearby Chuo Park). But despite what I imagine would be a flashy part of town, everything here is positively ancient. Crumbling old houses, 30 year old noodle shops, I even found a well for getting ground water.
Yep, this is my home.
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Tokyo, Shinjuku-ku, Nishi-Shinjuku 4-16-3
Closest station: Nishishinjukugochome
Open 11:00-15:00, 17:00-21:00