I often visit a customer site in Kokubunji, so I've stayed here on a number of occasions. It's a reasonably priced hotel, the rooms are clean and tidy, and it's the best Hotel in Kokubunji (it's just about the only Hotel in Kokubunji).
It's right on-top the JR-line station, but it's isolated enough so that you don't hear the noise, and form the station it's only 30 minutes to Shinjuku on the Rapid trains (which are about every 10 minutes).
If you're planning to stay a while consider upgrading to a suite (about 9,000 yen more), you virtually get a small apartment to yourselves with a living room, and dressing room.
There are plenty of shops and restaurants on your doorstep, so it makes a good base. If the weather is fine you can easily see Mount Fuji from Kokubunji, but I'm not sure the Mets has any West facing rooms, I've certainly never had one.
The breakfast is basic, but usually included in the room price (if you book direct in advance).
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