Technically, the Kruger ecosystem is a malaria area so I don't know if that will work for you.
The Madikwe is a malaria free reserve on the South Africa/Botswana border. It is about a four hour drive from Johannesburg. I rented a 4x4 and drove to Madikwe in July of this year with my wife and teenage daughters. We went to Sun City on the way back. Sun City is one hour from Madikwe and about three hours from Jo’burg. It was really too cold for water activities at Sun City but my kids, being from Minnesota, did them anyways! In Madikwe, we stayed at Madikwe Safari Lodge owned by More Hotels. At Sun City we stayed at the Palace.
Madikwe: Here are some other choices in the reserve but I am not sure of the kid’s ages:
Motswiri – Kids of any age
Madikwe Hills – You would need to stay at Little Madikwe Hills if kids are under 12
Buffalo Ridge – no kids under 12
The Bush House – kids of all ages
Eastern Cape – Malaria Free
Amakhala Game Reserve – Leeuwenbosch Country House allows kids of all ages.
Lalibela Game Reserve – Mark’s Camp has a childs program.
Kariega Main Lodge is child friendly; The Homestead is child friendly but you need to take the whole thing, 5 bedrooms.
Kwandwe – this was mentioned above.
I took my kids into Addo when they were 3 & 5 back in 2001. I was a submarine officer in the (US) Navy at the time and not in the safari business. We were visiting family in the Port Elizabeth area. Riverbend in Addo also is great for families and children of all ages are welcome.
The Eastern Cape in general is great for families as transfers between these three properties for example, can all be done by road, which is far less hectic than flying with children.
Near Cape Town - Malaria Free
Samara is great for kids and The Manor can be booked on Exclusive Use basis. Children under age 8 typically cannot participate in game drives:
http://www.samara.co.za/children.htm
Others:
Mashatu in Botswana six hours north of Jo’burg is also malaria free.
What is your budget? Is it is unlimited Tswalu is a fantastic option. Plenty of rhino.
Craig Beal – owner – Travel Beyond