In my opinion, the Mori Tower helicopter pad affords one the BEST views of Tokyo. With a 360 degrees and being outdoor, I couldn't have asked for a better view and a great photo opp.
I recommend going to the museum early afternoon then going to the observation deck. Totally worth paying extra to go to the rooftop. Even better, get there later afternoon so you can have both amazing day views and watch the sunset then start admiring the stunning night time views of Tokyo!