H.G.
As long as your son is healthy and doesn't show any signs of serious allergies, then take him! Ask your pediatrician if you can take a filled prescription for an antibiotic for ear infections, just in case he gets one. And also ask him/her what you should do if he gets a stomach bug, or something else like that. That way, you'll feel confident that all your bases are covered.
It'll probably be harder for you to enjoy the trip, with a little one along. But if you don't mind helping him nap and eat along the way (and lugging all that baby stuff!), then definitely take him! He may not appreciate Macchu Picchu yet, but he'll enjoy the time with you. :)