You can get a boat from Iquitos (Peru) to Santa Rosa (Peru) then Tabatinga (Brazil) / Leticia (Colombia) to Manaus (Brazil). You can choose either speed boats or local slow boats and some luxury liners. I took a speed boat from Iquitos to Santa Rosa and then a slow boat to Manaus.

I should mention that Santa Rosa (Peru) / Tabatinga (Brazil) / Leticia (Colombia) are all within walking distance of each other (but Santa Rosa is across the river and you get to the other side by a small water taxi)

Amazon Cruises are usually concerned with wildlife spotting in National Parks and aren't generally for travel. From Manaus, some recommended ones to consider are the National Geographic recommended Tucano Cruises:

http://thinkjungle.com/amazon-jungle...-amazon-cruise

and also Clipper Cruises for shorter trips:

http://www.amazonclipper.com.br/

In Iquitos, I thoroughly recommend a tour of the Pacaya Samiria National Park. And tours that do this are the Delfin Cruises:

http://thinkjungle.com/amazon-jungle-tours/delfin-i

and also Aqua Expeditions:

http://www.aquaexpeditions.com/

and then Jungle Expeditions:

http://www.junglex.com/en

In Iquitos, tour operators seem to like calling themselves "something" expeditions for some reason ... I imagine expeditions sounds a little classier than adventures, but I digress.

I spent most of my time in Iquitos as I found Manaus too large and noisy for my liking. I travelled from Iquitos all the way around then zipped down Colombia to run back to Iquitos for some more Amazon trips. When I get back I have to visit Tarapoto as I hear it's a little more off the beaten track. Happy travels!