Long-distance travel on cargo ships basically has to be booked in advance, and paid for handsomely, these days. It wouldn't probably be possible to find a ride just by asking around a port, as might still be the case from Zanzibar to the Comoros and on to Madagascar.
This site might give you some ideas of costs and possiblities!
It might be a longer voyage than you planned. The MV Ali Zulfikar (or a similar spelling) carrying passengers from the Comoros to Tanzania, has just been taken by Somali pirates. On current experience, they will be held on the ship off the Somali coast for up to a year - assuming the ship owners are (a) contactable by the pirates and (b) prepared to negotiate a ransom amount.
Otherwise the ship will be used by the pirates as a "mother ship", and the pax and crew will be drafted in as deckhands. "Up the Jolly Roger, me hearties!"