We most enjoyed our stay at Tambopata Research Center, operated by Rainforest Expeditions (they also carry out research and are advocates of preserving some of the Amazon environment and sustainable tourism with equitable involvement of native peoples). TRC is a bit more remote and rustic than some might prefer, but the hiking is great, the collpa stunning with its views of visiting psittacines (we aw, iirc, 13 species of parrots, macaws etc.)
Rainforest Expeditions operates three Amazon lodges: Posada Amazonas, Refugio Amazonas and Tambopata Research Center.