I used to love an nice memorable old-style kuro-buto near Ueno station, that I found by chance a few years ago. Now that I don't live in Tokyo anymore I don't remember exactly the location ...
Few searches on the web and I found this one, not so far from Akihabara district: Tsubame-yu, between okachimachi and ueno (3-14-5 Ueno, Taito). Looks classic and simple, but has even a website, check it out!