I haven't cruised on the Amazon river myself. I had a wonderful surreal week on a Bolivian river boat (the only gringo on board) in the Amazon Basin while traveling to the border of Brazil. You can read about the
river boat trip here.
Either in Iquitos or in Manaus it shouldn't be too difficult to get things arranged. Ask around while traveling, your fellow backpackers will be your best source of information on the road.