Fastest option is the Narita Express direct to Shinjuku station - about 3,100 Yen and takes about 75 mins. Leaves every hour from the station under the airport, and you have to book a specific seat before you board. There is a ticket office just at the entrance to the platform. From Shinjuku station, take the South Exit, then turn right and take the underpass to the Toei Shinjuku subway station. Buy a ticket and go just one stop to Shinjuku Sanchome station. At the ticket barrier, turn left, go to the end of the Underpass (exit C8 I believe) and you will come out in the BYGS building. This is very, very close to the Lornstar hotel.
If that's too pricey, you can take one of the regular trains for around 1,000 Yen. These have stops, take longer and get you only to Ueno station. Here transfer to the subway (in the same station) and buy a ticket to Shinjuku Sanchome (but this time the station on the red Marunouchi Line) - about 190 Yen. First take the orange Ginza Line to Akasaka-Mitsuke station, then make the easy change to the Marunouchi Line. This time, make sure when you exit the barrier to walk in the direction of the rear of the train. Here you are in the same long underpass system, so walk along till you come to Exit C8. Total journey time will be around 2.5 hrs. There are other ways but this is, I think, about the cheapest - and the least complicated!
In addition to Time Out's excellent city Guide recommended by Icon, you should purchase the Tokyo City Atlas: A Bilingual Guide. It's paperback, slightly larger than the Time Out Guide and invaluable for mastering how to find Japanese addresses.
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