The variety of hotels in Iquitos means that everyone from backpackers to luxury travelers will find a place that appeals to them. However, be aware that for every decent, clean hotel there is a run-down, noisy hole-in-the-wall, so choose wisely. Budget travelers, in particular, need to take care to find the few exceptional hostels among the less-than-desirable ones.
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 taxis. If you're staying for several days, you may want to reserve your first night in a more reputable hotel and then explore the area to find a nice budget hotel.
If you are looking for more immersion into the Amazon, a jungle lodge is just the thing for you. The lodges, which are generally close to Manu and Tambopata, are situated away from the city, offering a less tainted view of the jungle. Many of the resorts are all-inclusive, meaning all meals are included in the lodging price, often due to the fact that there are few or no places to eat in the area. The lodges all also offer guided excursions and other activities in the surrounding area.
Other Hotel pages in The Peruvian Amazon Basin that may be of interest: Yurimaguas Hotels, Jungle Lodges Near Iquitos, Tarapoto Hotels, Tingo Maria Hotels, Manu Biosphere Reserve Hotels, Moyobamba Hotels, Iquitos Hotels, Chanchamayo Hotels, Puerto Maldonado Hotels and Tambopata-Candamo Nature Reserve Hotels.