The only excursion we booked was the tree top lodge, excellent, worth every penny. Involves an overnight stay at the lodge. Food at lodge is as good as on board ship and room is an experience - a good one though. The ship is docked at Manaus overnight and I think you can book excursions during that period, but if you choose the lodge, that takes most of your time in Manaus. We returned from the lodge and dashed to see the theatre, which is within walking distance of the ship. Other stops along the amazon are easy as you are ferried ashore by boats and thats you there!! You will enjoy this cruise it is fantastic. Make sure you are on deck as you leave the sea and turn into the river, the water changes and all you receive all sorts of visitors on board!! Again book the tree top lodge, 1st class.
I did this cruise on the "Black Prince" some years ago. I wasn't aware that there were trips available on shore but that may be the case. Whatever you do make sure you go inland for there is so much to see. On an excursion from Manaus I stayed overnight in the jungle in a tree-top lodge which was a great experience which included an alligator hunt. On another day I went on a piranha fishing expedition which was great fun. As the river is so enormous there isn't much to see from the ship.
Whether you take a company-organised excursion or do you own thing I am sure you will find it a memorable experience.