Wow! So many options and so many of them bad.

For this trip, I'd eliminate the whole Skyliner + Yamanote Line option. The Skyliner is fine but the Yamanote during rush hour with several pieces of luggage would be a nightmare. And, has been stated, the cab distance from Nippori or Keisei-Ueno is much more than from Tokyo Station.

Either take the Narita Express to Tokyo Station and grab a cab or use the limo-bus. Let the professionals do the navigating.