Within the Peruvian Amazon you will find hotels and lodges mainly in Iquitos, Manu and Tambopata.
There are a variety of hotels in Iquitos, and everyone from backpackers to five-star travelers will find a place to stay that appeals to them. For every decent, clean hotel, however, there is a run-down, noisy hole in the wall, so choose carefully. Budget travelers, in particular, need to take care to find the few exceptional hostels among the less-that-desirable ones. Do some research before arrival: visit web sites, look at photos and read the comments made by previous travelers.
Once you’ve made up your mind, make reservations, as the best places tend to fill up. Also, if you make arrangements ahead of time, your hotel may pick you up at the airport, saving you the hassle of dealing with cabbies. If you’re staying for several days, you may want to reserve your first night in a more reputable hotel, and then set off to visit less expensive places. To see all hotels in Iquitos see the Viva Travel Guides Iquitos Hotels Guide.
In Manu and Tambopata you will find a selection of Jungle Lodges. Many are all inclusive, and offer tours around the premises. You can find a list of all lodges in Manu on Viva Travel Guides Manu Lodging Guide.