HND is in Tokyo and NRT is about 90 miles from Tokyo. There are many affordable options to get to and from NRT if you find better fares there. I took the airport limousine bus and was dropped off and picked up at the hotel. http://www.limousinebus.co.jp/en/

I stayed at the Hotel Metropolitan and enjoyed my tiny room. http://www.metropolitan.jp/e/

The Tokyo Subway is very nice and reliable. http://www.tokyometro.jp/en/index.html

I hear good things about the trains, but did not ride any when I was there.