Originally Posted by
balowlyblue
Agree wholeheartedly with this- may also be worth looking at the "Airport Limousine" transfer bus if you are laden with bags- highly efficient transfer service serving all the hotels.
I would recommend taking the Friendly Airport Limousine bus too. From Narita it is about 3000 yen and from Haneda about 1800 yen - if I remember correctly. To Shinjuku it is 1hr30-2hr and from Haneda about 50mins-1hr.
You can buy tickets from the counter inside the airport and then pick up the bus at the relevant stop right outside the terminal. They take your luggage from you there and hand you a coupon which you need to reclaim your baggage from the bus.
They stop at several hotels in Shinjuku, although from experience most Shinjuku hotels are within walking distance of the Shinjuku Station stop.
I have used them many times and can never fault the service - it also saves the hassle of carting luggage through busy stations too.