Coming up or down the main part of the Amazon, you will see very little wildlife because of the width of the river. If you're interested in Amazonian birds, mammals and reptiles, I'd HIGHLY recommend staying a couple of days at one of the jungle lodges just upriver from Manaus before flying home. We stayed at the Ariau Jungle Towers, the only lodge built at treetop level (much better for animal spotting), and saw several kinds of monkeys, sloths, constrictors (not anacondas), caimans, freshwater dolphins and birds galore. We even fished for piranha--cheesy but fun. We went caiman spotting at night, hiked during the day and even visited a local village. Despite being somewhat touristy, it was a great experience.
Your plane will likely go through either Sao Paulo or Rio, then Brasilia, before landing in Manaus (and the same in reverse). From Sao Paulo it's between 1-2 hours from there to Brasilia, and then another 1-2 hours to Manaus.
The Amazon is like no place on earth.
Bring candy with you to give to the children. It will be very appreciate.
The cruise down the Amazon is a very interesting one. The city where you start the cruise is also unusual. I think that the whole experience was really worthwhile. We did not do the overnight jungle bit because it was a long flight with changes and we thought that we might not get the benefit of that kind of excursion particularly as you needed to stay awake through some of the night. Those that did said it was brilliant but tiring after all those flying hours and they wished they had had more time for the experience. I did play water polo with some of the local lads in the hotel pool and even though the day was very cloudy got quite sun-burnt, I forgat we were actually on the Equator....hope that helps your thinking, Neil Dow.