In the end, it will depend on your travel itinerary as you may go to the jungle in advance of or just after your tours in Cusco. From Lima to Iquitos you'll have a lot more flights out there and probably also less costly types than from Cusco to Iquitos. https://peruamazonjungletours72604.ageeksblog.com/26293737/new-step-by-step-map-for-peru-amazon-tours-from-cusco