Well you are in luck there are lots of great lodges in both National Parks.
Our favourite lodge is located in the Tambopata region about 2 hours along river from the main Jungle town of Puerto Maldonado. Rainforest expeditions run a lodge called Amazionias Lodge which is superb. check-out their website and let us know what you think. 4 days / 3 nights package is best. Pricing is competitive.