Most hotels will arrange pick-up from the airport.
To get from Kilwa Masoko to Kilwa Kisiwani you will need to take a boat. Up market hotels will organise this for you and charge you alternatively you can organise this yourself as there are boats waiting at the dock that you can charter. Expect to pay around 10'000/- to 15'000/- for a sailing boat to drop you off, wait and then return you to Kilwa Masoko - more for a boat with an engine. If you don't speak Swahili you can hire a guide who you will probably want to show you around the ruins who should also take care of this, but bear in mind that the guide may not always try to get you the best price.
To get between Kilwa Masoko and Kilwa Kivinji there are shared taxis regularly, although if you turn up they will probably insist that you have to hire a private taxi or you will have to wait hours and hours. If you politely decline and offer to wait they usually leave every half an hour or so.
All three towns are small enough that the best way to get around them is by food although see the safety section. There are a number of taxis and tuktuks bajaji around town if the heat is too much for you.
