I have been up the Tokyo Tower main observation deck, TMGB and Landmark Tower in Yokohama. I don't think the views differed too much. TMGB is free, but the observation level has cafe and gift shop in the middle, and creates considerable reflections and glares if you plan on taking pictures. Tokyo Tower's main observation is kept dimly lit at night so you can take in the night view better. Out of these three, I liked the Landmark Tower's views the most. I liked the location right up against the Tokyo Bay, and I went there during a clear day vs evening for Tokyo Tower and TMGB.
I haven't been to Sky Tree, and after learning of the admission price, I don't feel I need to go there that badly.
Other skyscraper observations decks in the area are: Roppongi Hills (Roppongi), Sunshine City (Ikebukuro) and Tokyo World Trade Center (Hamamatsucho).