Tokyo Government South Observatory 東京都庁 南展望室
Similar to the North Observatory, the South is free as well, but gives a different view as it is located in an adjoining tower. The South Observatory is closed on the 1st and 3rd Tuesday of every month and hours of operation are shorter than the North: 9:30 - 17:00. However, on days that the North observatory is closed, they extend the hours until 23:00.
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Fantastic (and free) views of Tokyo from here. From memory, this was the quieter of the two observatories (North and South). Shorter queues, fewer people. Was lucky enough to go on a beautifully clear day with Mt Fuji in the distance. Great experience. There is a cafe here too, why not have a coffee in the clouds..?
A great view for the price of-- oh! It's free! There are cute souvenirs at the top, though are relatively pricey in comparison to other locations.