The Pit Inn remains near, or at the top, of any list of live jazz venues in the Tokyo area. 2015 saw an ongoing series of shows celebrating the club's 50th anniversary, and it shows no signs of slowing down any time soon.
Unlike far too many jazz clubs these days, the Pit Inn puts the focus squarely on the music. All seats face the stage, and the audiences are mostly dedicated fans who don't spend half the show talking or fiddling with their phones. The atmosphere is exactly what you imagine an old, basement jazz club in Tokyo would be; old posters, dark lighting, 'minimal' service. The only minus point for me is the lack of a good beer menu.
The style of music varies so check the schedule in advance; their English language web page always has a full description of the featured band so it's easy to find the type of gigs you want to attend. No other club in Tokyo features as many of the best local musicans so let's hope they keep going for another 50 years. It's a cliche but true: the Pit Inn is the Village Vanguard of Tokyo.