I haven't done an AirBNB ourselves (generally like a hotel where people just take care of everything for us). But personally, I'd try to be close to a subway station - preferably along the Yamanote Loop Line. You can certainly be along another line but I find the Yamanote line better tourist wise given the large circular route it takes to hit many major spots or to quickly do a hop off and on to another line.
If you haven't saved this to your phone already, you should. Note the station numbers so you can tell your direction as you go. Stations that are grouped together can be accessed (mostly) underground by just walking.
http://www.tokyometro.jp/en/subwayma...en_en_1702.pdf