I took my bike to Zanzibar and it was a nightmare getting it off and on the boat. I asked around a lot to find a boat that had some sort of ramp and was lied to in both directions. They get a ton of guys to lift and lower the bike 15 feet or so into the boat, picking it up by mirrors, fenders, lights etc. Stress. It even got soaked by a leaking shipment of vegetable oil. Then it's on the boat and you can't get it off by yourself on the other side so they charge extortionate rates to help. I even got the Captain involved, but he was on their side.
You can cruise up to Bagamoyo (which is a nice, quiet place to visit). Go to the Bagamoyo Beach Resort and leave it inside the house of the French guy that runs the place for free. He will even arrange a dowh out to Zanzibar for you (which it is technically illegal for foreigners to do).
Zanzibar is definitely worth a visit, but not with the bike if you ask me.