Hi Hazarrd,
You should be aware that "F3008" is almost certainly a cover for the guide and/or company whose services he's recommending. At the moment he's "ken", but in the past he's used three or four other names, and always recommending the same people, often without answering the poster's question.
However, he is right when he says there's no ferry from the African mainland to Madagascar. Cargo ship is theoretically possible, but is very much a hit and miss affair - you'd be very very lucky to find one going and willing to take passengers at a time that suits your plans - on your time scale, it's not a realistic option.
You can fly from Johannesburg to Tana or Tolagnaro/Fort Dauphin, or from Mozambique, you could also fly up to Dar es Salaam and from there on to Moroni in the Comoros, where you can get a flight to Mahajanga. (For schedules, check the websites of LAM, Air Tanzania and Air Mad).
Flying via Mauritius doesn't seem to be a sensible suggestion. To get a flight there, you'd have to go to either Johannesburg or Nairobi, and as there are already direct flights from Jo'burg and there will be again from Nairobi from October/November, there's no obvious reason for going the long way round via Mauritius (unless Air Mauritius offers a very favourable deal).
