The lake is large enough that you cannot really "tour" it — pick a base and explore from there. Ferries run twice daily between San Jorge (near Rivas) and Moyogalpa on Ometepe, the workhorse crossing for backpackers and locals; the journey takes about an hour and costs a few dollars. A second route from San Jorge serves San José del Sur. Cars can be loaded on the larger ferry but you should book ahead.
A second slow ferry runs the length of the lake from Granada to San Carlos at the mouth of the Río San Juan, stopping at Altagracia (Ometepe) and the Solentiname islands. Schedules are sparse — typically twice a week — and timings change. From San Carlos the Río San Juan continues by lancha down to El Castillo and on to the Caribbean.
Smaller boats — pangas — can be chartered for short trips around the Isletas, to Zapatera or to specific Ometepe beaches. Negotiate the price before you step on board.