There are good AirBNB's close to Ikebukuro, Shinjuku and Ueno, all on the Yamanote loop. I second the idea of staying on this loop because it has access to all the major areas you're going to want to see. I stayed in an AirBNB about two blocks from Ikebukuro station last time and while the quarters were cramped and I wouldn't do it again, the location and price were awesome.
One thing to keep in mind that, as a Westerner, don't just look at the pictures of the AirBNB you're interested in. Look and see if the square footage is sufficient; it can be hard to operate in these rentals if you are a tall/big person. Try and avoid long, narrow rooms and try for square layouts; you'll thank yourself later.
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