ShinKouYou is a small, crowded, very chummy and "after-work" type of place located in a office building basement right around the corner from Yodobashi Multimedia Kan in Nishi Shinjuku, west of the station. I went there with my coworker Machida-san after picking up some computer parts we needed for work at Yodobashi. Many visitors like to go to Akihabara to see the electronics district but you can also have a lot of fun in the Yodobashi Camera area just west of Shinjuku station, there's a number of places to eat and drink there too and it has a loud street market type of atmosphere. There are various Yodobashi specialty shops there including one shop dedicated to electronic dictionaries, that's where I bought mine and I got a pretty good deal. In any case, ShinKouYou has very nice tables and benches made out of polished wood. A square counter is in the middle of the room and there are two or three tables for four around it. Very loud with the various cooks and employees shouting all sorts of things to each other. We had the paiku (ぱいく) tsukemen and ramen respectively, the paiku idea was new to us, it is sort of like tonkatsu but with much more thinly-sliced pork, and very finely breaded and salted. Sort of like weinerschnitzel except with pork. The broth is a Tokyo-style shoyu broth, except slightly stronger than usual, it contains green beans and chopped negis. The noodles were served on an interesting bento-like noodle tray, however the amount was a bit small, and they were fairly thin. The hand-made gyoza were good and larger than you usually see. There are other options that I might consider in this area but this would be a respectable choice for sure.
Masshi's Gourmet Diary page
Diddlefinger Map (English labels)