excuse the delay in responding!
So we took a boat from agencies that sell directly there at the output port in Bethlehem. Unfortunately we do not have agency contact to get you (unless the name of the Member who is in the post, al perhaps searching the internet you find something) because they are really messy. The sale service and shipping provided by them is of poor quality and disrespectful. But, unfortunately, foram as únicas opções que encontramos naquela época.

As for the tour itself, took almost 6 days upriver from Belem to Manaus. This boat is like a bus or train. Will stopping in cities that are on the waterfront. And there go up and down passengers, o barco fica parado de 30min a poucas horas em cada cidade dependendo de quanta carga sobe no navio.
It is worth bearing in mind that it is not something tourism itself. It is a means of transport, then there is no comfort. Bathrooms are shared, areas also, a limpeza é mínima e algumas condições para as pessoas não são dignas como deveriam ser.
But for us it was very interesting to live this reality and familiar with the people there were there. If you have that in mind and know enjoy the beauty of the way and the fact meet very nice people, vale a pena!!
For you familiar with the cities on the way might fall in some cities and stay a few days in each. Santarém, for example, gets in the way and it's a big city compared to other. But to see how these work stoppages, would have to talk directly to the company selling the services or buy the ticket for parts. Sempre de ida.
With respect to take the boat in Bethlehem and buy the plane back in Manaus really think the best option!! Go back and forth this way at one time would be too tiring! Believe! hahaha

Esperamos ter ajudado.
Best wishes and good luck, because really the cuisine of Pará and northern Brazil is VERY different and special!!!