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.
- Ferries are the main form of transport used for crossing the lake border. Ferries ship both passengers and vehicles.
- 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 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.
- 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.