There's no better place to stay in Tokyo than Grapehouse Koenji! Not only is Koenji a very cool place to check out (lots of restaurants, bars, music venues, and shopping!), but Grapehouse is also conveniently located near the Chuo Line so it's easy to get to just about anywhere in Tokyo.
Grapehouse Koenji has a sweet, clean, natural style--the tatami mats and wooden bedframes fragrance the common spaces with a wonderful woodsy scent, and the minimalist decor is sprinkled with mementos from other happy customers.
Sanae-san's cooking is top-notch, so I also highly recommend trying breakfast at least once!