There's a big harbour in Manaus, with ticket offices where you can buy passages to the boats that depart Manaus in either direction. Prices are not expensive, and you can usually choose between a hammock or a small cabin with private WC.
(I am talking about passanger boats and not cruise ships. If you want cruise ships, I don't really know where to catch them. But I think certainly not in Manaus. Just a thought though.)
The only question is, buying at the official ticket offices is not the best option, as the boat will stop for four hours 300 meters after it departs to let some 200 people get in, who bought the tickets somewhere else for half the price.
Unique Suggestions: That's why our boat left with so few people inside - and honestly, we were 250 at the end of the trip, 239 brazillians and 11 foreigners.
Guess who were among the 20 people that left from the first pier?
Yep, you're right.
Fun Alternatives: So what you should do, is what I sadly didn't do: follow the guys in the harbour who keep mobbing you and buy the ticket from them. You will then be taken to the other harbour, and hop on the boat for half the price.
I didn't do it myself, so yes: I guess you may as well be robbed. But well, some of you may be willing to take the risk.