We've stayed at three in South Africa which were spectacular: Phinda (twice), Londolozi
and Singita. Phinda and Londolozi both are affiliated with Conservation Corporation Africa (CC Africa), whose website is here:
Singita now is independent; its website is here: http://www.singita.co.za/intro/frame.php
Phinda is in KwaZulu Natal; Londolozi and Singita are both near
Kruger National Park.
In Botswana we stayed at Khwai River Lodge, which has undergone substantial renovation
since we were there. Its website is here: http://www.africangamelodges.com/gametrackers/kwai-river/
We have not stayed at either of CC Africa's lodges in Botswana.