All the prices quoted are per person and all-inclusive (unless otherwise noted), covering food, lodging, US$45 park entrance, and airfare between Cusco [1] and Boca Manu. Follow the links for contact information and more detailed information about each agency.
Links:
[1] http://www.moon.com/destinations/peru/cusco
[2] http://www.moon.com/destinations/peru/the-amazon/manu-biosphere-reserve/manu-agencies/manu-nature-tours
[3] http://www.moon.com/destinations/peru/the-amazon/manu-biosphere-reserve/manu-agencies/manu-expeditions
[4] http://www.moon.com/destinations/peru/the-amazon/manu-biosphere-reserve/manu-agencies/inkanatura
[5] http://www.moon.com/destinations/peru/the-amazon/manu-biosphere-reserve/manu-agencies/pantiacolla-tours
[6] http://www.moon.com/destinations/peru/the-amazon/manu-biosphere-reserve/manu-agencies/caiman-tours
[7] http://www.moon.com/destinations/peru/the-amazon/manu-biosphere-reserve/manu-agencies/other-agencies