There are a only 8 tour operators who have the licence to take tourists into the reserved zone. Tours start from Cusco and usually take between 4 and 10 days. Prices range between 500 USD and 1800 USD depending on the length of the trip and the operator. All tours are guided by studied biologists this is a rule by the park administration.
Be careful when booking your trip and try to book directly with one of the operators, as travel agencies will happily sell you the tickets, take a massive commission and just book you on a tour with an operator you don't know in advance. Make sure to ask about all the tour details before you book accomodation, extra fees, english-speaking guide if needed, food, jungle walks, other activities. Also try to bargain about the price!
Tour operators that offer tours into the reserved zone:
SAS Travel
Expediciones Vilca. With a price of around 700 USD for an 8-day tour one of the cheaper operators. Nonetheless reliable and excellent value we had an awesome tour with a great guide, a fantastic cook and lots of animal sightings
Pantiacolla. Rather expensive tours guided by a dutch biologist.
Amazon trails peru. probably guided by the best guide in the Manu National Park or ask for Abraham Huaman
A full list of tour operators and their tours can be found here: (http://www.perutourist.in...).