Iquitos or Puerto Maldonado?
 

I hear that you get the same type of environment in Puerto Maldonado but I hate to miss the "Amazon." However considering my current route. Lima>>Cusco>>Arequipa - fitting in Puerto Maldonado would be simpler.

Advice?

Then go to Puerto Maldonado. I haven't been, but have friends who have who like it a lot.

I've been to Iquitos and it is really the Amazon. But I wouldn't go back.

Even Puerto Maldonado is Amazon Basin, the Amazon river can be seen only in Iquitos. Iquitos is more expensive and to really enjoy it you should have to take a cruiseship to go around Pacaya Samiria National Reserve, there you can see Pink Dolphins, Black Caimans and maybe an Anaconda. If you use the lodge nearby Iquitos, you will see more natives than animals. That is why I like Puerto Maldonado or better to say Tambopata National Reserve, because it cheaper and it is easier to see animals: Well, to be honest I been there 2 weeks and I had the luck to see black caimans, a lot of macaws which are in dangerous of extintion and a jaguar.

In order to perform a circuit, Puerto Maldonado (Tambopata) is the choice.
In order to keep a low budget, Tambopata is the choice.

Well I hope this help you.