There was an Air Madagascar flight between Mahe Island and Antanaarivo but I don't know the status now. Air Madagascar website is down.
I am a frequent visitor to Seychelles and have not yet visited Madagascar-but I have several friends who have-and all are full of praise. If you have never been to Seychelles, it is an absolutely must see. It is unspoiled by mass tourism and it is truly the garden of Eden. Seychelles are very expensive- even for Americans but the sheer pleasure you will get visiting there will be worth every penny. Mahe Island is a good starting point for a few days then a stay on Praslin or La Digue.is highly recommended.You can visit the Vallei de mai-virgin rainforest with the coco de mer- It is the best tropical paradise on earth -in my opinion. I would recommend you stay in self-catering accommodation or if you mail me I can recommend some good small well priced hotels. The only way of getting there from JNB is on Air Seychelles, and it is a 5 hour flight on a cramped 737-800 ETOPS.