We've stayed at the Intercontinental at the airport (and at the one at Sandton as well as the Crowne Plaza in Rosebank). Primarily as I have tons of IHG points so we stay free. As I have status with IHG, we are always upgraded to a premium room. All three of these have nice rooms and are clean, secure and we experienced very attentive service.
The Intercontinental at JNB is a very nice hotel. But I personally would not pay the published rates for the rooms (approaching $300 USD). The restaurant is great for breakfast but we have had mixed experiences with it for other meals.
My son has stayed at the City Lodge at JNB and he liked it. It is one of the more reasonably priced hotels at JNB, the last price I saw for it was $100 USD. He thought the rooms were clean comfortable and more of a basic hotel room. But he says he would stay there again.
Both the Intercontinental and the City Lodge are walking distance from the JNB terminals. So these are good for arriving in the afternoon and departing the next morning.