Where in Tokyo are you traveling to? For views, I'd take either train over Limo Bus. The bus travels primarily on expressways that have limited views in many areas due to fences or being down in the ditch. Views are mainly unobstructed from trains. You may not find the scenery all that exciting on NEX or Skyliner, although you're up close to houses and forests and streets and people from your train window and so you get a glimpse of everyday Japan.

On either train, much of the first portion of the trip as you depart from NRT will be in farmland, wooded areas, etc. Skyliner speeds along over a vast farmland along a lake at one point. If you're on NEX, as you get closer to Tokyo, being on the right side of the train gives you a great look at the Tokyo Sky Tree. NEX goes underground just before the Tokyo station and stays in the tunnel until ~Shinagawa. Then depending on where your final destination is, you'll get different views beyond that. View-wise, it's pretty much a toss-up between NEX and Skyliner, although a slight edge goes to NEX because a).Sky Tree; b).tends to slow down more often which affords better look at buildings, streets and people outside.