Most operators in Paraty offer tours in a 4x4 or a schooner. Paraty Explorers covers similar areas but allows you to do it in more environmentally friendly way, and you get some good exercise along the way!
We took a bus and small boat and hiked up the Mamangua Sugarloaf (reviewed separately). Other excursions are available.
They offer walking, kayaking and stand-up paddleboarding. Don't let Google fool you - they don't have a physical address, so a phone call is the best way of getting through to them. They are very accommodating and Michael, our guide, was friendly and helpful.