I am sure you can travel in a way that is super interesting and not too stressful for you son. This would mean flying the long distances between southern Peru and Ecuador, staying in nice hotels and don't travel too far overland every day in a rental car. But of course, all that has it's price.
If you want to use public transport and stay in cheap hotels it becomes a bit more stressful. I never traveled at night, but there are still some long bus rides during the days.
I am sure the animals on Galapagos would be very interesting for a six year old. Inca ruins maybe less so.
I think the weather in Ecuador is similar most of the year, but in the South of Peru it is much colder in the winter. So depending on when you go, you may want to go to Peru in the period that is closer to summer (our winter). On the other hand, Machu Picchu is less busy in the low season and the Inca trail is closed in February.