We used this chain a few times when in South Africa
http://www.citylodge.co.za/index.php
They basically have 4 different types of hotels, Courtyard is the best, City Lodge, Town Lodge and Road Lodge. We actually only stayed in a Town and Road Lodge property (Joburg airport and Rivonia), but the City Lodge at the V&A was in a fantastic location just a short walk from the waterfront itself.
Might be worth a look, or even for other properties closeby? In Cape Town we slummed it in a Hostel, paying just £18 a night but it was the start of a 9 month round the world trip.
As for Joburg Nivsy, if you find you have to stay there head to the area of Sandton instead. Nicer and safer area apparently (we enjoyed it for a couple of days anyway).