I love Iquitos city for private reasons. Actually all depends on what you are looking for.
If you are looking for jungle lodges, I've read there are some very good lodges. However the best are in Puerto Maldonado area (Tambopata reserve), not Iquitos.
Do a research about trips to Pacaya Samiria, if you are looking for adventure and nature.
Besides, I've read also about very good jungle cruises that depart from Iquitos, some of them go to the Amazonas near the border with Brazil.