In the long run, it will depend on your travel itinerary as it is possible to go to the jungle right before or just after your tours in Cusco. From Lima to Iquitos you'll have much more flights obtainable and doubtless also less costly types than from Cusco to Iquitos. https://manu-peru-amazon-tours82604.webbuzzfeed.com/26853795/peru-amazon-river-tours-fundamentals-explained