Herbie is the kind of jazz bar you stumble upon randomly on the way home some night and end up staying in for three hours. Located in unfashionable Machida (about 25mins south west of Shinjuku on the express Odakyu Line), it's a tiny basement bar that seats 20 people max, though it's rarely that full. The room is a small rectangle with a mix of counter seats and 4-seat tables, but is more suited for quiet drinks & jazz time rather than a noisy get-together.
Owner Fukuoka-san is a cool cat with a taste for whiskey; there are 75 different brands of whiskey, bourbon and rye behind the bar. The music is anything from classic jazz from the 50s up to current releases; last time there I heard some 1990s fusion back to back with Horace Silver. Although you wouldn't think it, Herbie does host the occasional live gig; check the website for the schedule. It's a fairly dark room and may be slightly claustrophobic for some, but it's pretty much a perfect neighborhood jazz bar to hit after dinner or for a late night-cap. Look for a picture of Herbie on the wall near the door, otherwise it's mainly Miles on the walls.
More pics of Herbie here at Tokyo Jazz Joints.