Any stop you see to the LEFT of Shinjuku Station are LIMITED very limited services, sometimes it is only seasonal.
The best way is just take the Narita Express to Shinjuku Station, then change to a regular JR train (CHUO LINE Rapid Service) to Mitaka Station (about 15 minutes ride from Shinjuku) so it is not too far.
Use the ticket called SUICA & NEX, it is on the JR website, the price is fixed plus you get a suica card so its a good deal.
If you have luggage, it's probably better to take the NEX to Tokyo Station, ride the escalators from the basement platforms up to the Chuo Line platform (basically right above but about 6-7 floors apart) and take a commuter rapid from there. The Chuo Line (orange commuter rapid) trains originate from Tokyo Station on an elevated platform above the renovating Tokyo Station Hotel on the Marunouchi (west) side of the station. You can usually get a seat, but at least if you can't you can easily get space for any luggage you might be carrying. This train departs frequently and fills up fast and is usually quite crowded when it pulls into Shinjuku Station. Some people get off at Shinjuku but a whole lot more are getting on. Try to get a spot near a door so you can get off easily at Mitaka. Depending on the time, this train can get extremely crowded. It will be empty at Tokyo Station when it starts, though. You just need to queue up in line and hope you can get a seat.
I agree. Take the NEX to Tokyo, change to the Chuo Line to Mitaka.
One more thing, at Tokyo Station, it's all escalators or elevators getting from the NEX (Sobu/Yokosuka) platforms up to the elevated Chuo platform so having luggage is not a problem at all. See this map: www.jreast.co.jp/e/estation/e_tokyo.html
You will come in down on B4 (dark green platform at the bottom), come up the escalators (follow everyone else) towards the Marunouchi Central Exit and follow the signs into the main station concourse to platforms 1&2 (darker blue and elevated on the map) which will clearly be marked with orange Chuo Line signs.
The station is extremely daunting and intimidating to a first time visitor. Just follow the signs carefully and you shouldn't have problems. If you get lost or have questions, just ask someone where the "Chuo Line" is and they will direct you to it. As you go up the escalators to the platform, to your left side will be the east side of the Tokyo Station Hotel (undergoing renovation).
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