I would suggest the Limousine bus, they are available both from Haneda and Narita, it is a luxury bus with plenty of room for luggage and they stop at most of the Tokyo hotels including the Hilton (Shinjuku one, great, we are there in December again).
This will definitely save you some cruise $'s especially if you book your own hotel.
If you can choose Haneda is a lot nearer than Narita.
We found the underground quite friendly to use to plan our trips just get a good map and people are always friendly and willing to help.
Happy planning
Rosalyn