Years ago I hitched a lift on a sailing boat from Zanzibar ( I was cycling ) and made it to Moroni on Grande Comore in the Comoros Islands. I then hitched lifts on passing barges and cargo ships to make it to Anjouan, Mayotte and eventually Nosy Be on the northwestern coast of Madagascar. I stayed on the island for a while ( it is wonderful ) and found a Mauritius-bound cargoship. It is certainly doable but you will need time and patience. There is very little cargo traffic between Mozambique and Madagascar ( I was just there and investigated, just in case ). Your best bets are definitely Durban ( all the Indian Ocean Islands import their wares and some of their food from SA ) and to a lesser extent Dar-Es-Salaam/Zanzibar or Mombasa. If you do find a boat to Madagascar or any of the islands make sure you can prove that you have a ticket OUT of them or they won't let you disembark.
Hope that helps.
L.
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