The main danger in the jungle surrounding Iquitos is the same as any tropical zone: Malaria. There is very little malaria in the city, but it is common outside the city in the jungle. You should get anti-malaria pills from a doctor before your visit. Malarone if that's what you've been prescribed should be taken two days before arrival and 7 days after leaving. Bug repellent can be purchased in pharmacies anywhere in Peru and should be applied liberally whenever going out, and especially if taking an Amazon tour.
Yellow fever vaccine is also recommended.
government tourist and assistance office, iperãº
The Peruvian government features a free service that gives official information on the different attractions and assistance in case the service rendered does not comply with the one agreed by you. You may write to iperu email to plan your travel and ask them for the record of the tourism companies that you consider.
iperú service is unbiased and extensive. Jungle tours are available on every street but if you want to go to a reliable operator then use those recommended by the tourist office. The office is not much to give you confidence but once you establish contact you will find the staff helpful and knowledgable.