There is only one right way to do this transfer:

• Skyliner from Narita to Keisei-Ueno (way faster and cooler-looking than any other option into the city)
• Check out Ueno Park and/or Ameyoko
• Yamanote Line from Ueno to Hamamatsucho
• Walk to Zojoji temple and get a photo with the Tokyo Tower in the background
• Monorail from Hamatsucho to Haneda

For a first-time visitor to Tokyo, taking the subway is a total waste. Stay above ground so you can see things. For the same reason, monorail >>>>[unscalable wall]>>>> Keikyu.