The building stands right opposite Kyoto Station and also houses restaurants, stores, a spa, and a 3-star hotel, Kyoto Tower Hotel, where we stayed for four nights. If you don't mind the somewhat-80's-vibe coming from the hotel furniture, I'd recommend it, as the location is incredibly convenient in terms of catching public transport, the central bus station being right between the hotel and the train station.
Plus, you get a free ticket for the tower's observation deck!