Amazon Eco Adventures is an excellent choice, offering tours with small groups, comfortable speedboats, their own overnight boat and top guides. You’ll go swimming at the meeting of the waters, and activities like visiting indigenous villages don’t have a voyeuristic feel. Their trips to Presidente Figueiredo are equally rewarding, forgoing the touristy waterfalls for caves and falls where few visitors go.
They also have a lodge up on the Rio Urubu. Although they're pricier than others, they're well worth it.