How to cross borders from Uganda, Tanzania and Kenya at Lake Victoria
It's actually pretty easy.
From the Kenyan side, the main crossing port is at Kisumu.
In Uganda, you can use either Jinja, Entebbe or Port Bell.
In Tanzania, the main ports are Mwanza, Bukoba ( the ferry between Mwanza and Bukoba is also now operational and saves you up to 4 hours of driving) and Musoma.
There are also several small ports though from where you can cross especially on the Tanzanian side.
Ferry transport
Ferries are the main form of transport used for crossing the lake border. Ferries ship both passengers and vehicles.
Ferry duration.
A typical ferry ride like the one I took from Port Bell( Uganda) to Kisumu (Kenya) takes 13 hours, and from Port Bell to Mwanza( Tanzania) takes 20 hours.
Fares
Fares pretty much differ per route, per season and per ferry service provider so I can't know what the exact fare currently is though it should range between $30 and $50.
Visa requirements
I hold an East African passport so I could just cross freely across all 3 countries, for non-East African passport holders you have to make visa arrangements with all respective embassies of all 3 countries.