If you want to be looked after throughout the trip, you can opt for a shared-safari, and get one hell of an itinerary prepared for you. If you are more on a budget trip, or if you want to explore the Kenya more locally, then public transport is your best option.
Ferry ride is not very common in Kenya. The Likoni ferry run throughout the day and night, between the mainland and Mombasa Island. It is cheap, and is free foot passengers.
A municipal bus service is effective only in the capital, Nairobi, though people rarely use it. The Matatu, or private buses and mini-buses, are the most common modes of public transport in Kenya. They are more reliable, cheaper, and, contrast to popular belief, is safer too.
Taxi service is very cheap, and easily available in even the smallest towns of Kenya. In the larger cities like Nairobi and Mombasa, taking a taxi during nights is virtually mandatory.