If you are willing to pay the price, I recommend the Tokyo City View over the Tokyo Tower. It always seems to be less crowded, it is more stylish, and there are lots of places to sit and really get a good look at the city. Go right at sundown for the best views.
Inside, the 'Sunset Cafe' serves coffee, tea, juice, beer,... There is also the 'Mado Lounge' - haven't been inside, but it looks pretty fancy. They regularly have live music and special events, and I believe it is available for private parties (although I bet the cost is pretty high).
Hours of Operation: 9:00 to 1:00 am, open everyday
Admission: Adults 1,500 yen, high school and college students 1,000 yen, children 500 yen.
For English Information: http://www.tokyocityview.com/en/index.html