In the end, it relies on your journey itinerary as you can take a look at the jungle ahead of or after your tours in Cusco. From Lima to Iquitos you will have a lot more flights offered and possibly also much less expensive types than from Cusco to Iquitos. https://manu-peru-amazon-tours60481.humor-blog.com/26332374/the-peru-amazon-tours-iquitos-diaries