My only knowledge of this is mosquito's cannot survive with aircon, so you should be 'safe' on board. Regards.
I have made this trip and strongly recommend taking anti-malarial tablets. You must also have a yellow fever innoculation. This disease is common in the Amazon jungle. It is essential to go ashore on this trip for little can be seen from the ship. If you can do an "overnight" in one of the jungle lodges accessible from Manaus you will find it a great experience. I loved it.
The diseases below may be a risk in all or part of the country and are presented alphabetically:
Cholera, Diphtheria, Hepatitis A, Hepatitis B, Rabies, Tetanus, Tuberculosis, Typhoid.
I would add Yellow Fever to that list > .... Neil.
Malaria kills over 3 million people a year in Asia & South America so take the tablets before/during/ after your cruise you should talk to your doctor at very the least 3 weeks before your cruises departs, mosquitoes are most active at dawn /dusk but if they are disturbed they will bite at any time.