The Room is one of Tokyo's best clubs, if not THE best for fans of funky/groovy music. It's home base for the Kyoto Jazz Massive and owners the Okino Brothers often DJ there, alongside DJ Kawasaki and Tokyo's funkiest DJ, Kuroda Daisuke.
There are frequent live performances as well (very crowded) and the vibe is kept friendly and not at all elitist by manager Sato-san. The Room needs to be your first stop if funk and funky jazz is what you are looking for. Events almost every night so check the homepage; some may feature Latin/House/Hip-Hop DJs and not funky jazz.