What to expect
A hotel in Iquitos, a lodge and a riverboat make three different trips. Start with where you want to spend your days. Allpahuayo Mishana suits a focused forest visit; Pacaya Samiria needs room for the approach through Nauta and time on the river. A longer wildlife list on a website does not make a better trip.
How it fits into a journey
Choose one main stay. Add Iquitos before or afterwards and treat Allpahuayo as a separate outing, not a quick stop with all your luggage.