Hi, I know that this is a really late reply but if anybody else is looking at this with the same Q, then they may want to know.
I volunteered with Santa Martha Flor de la Amazonia (the Amazon one) for 6 months and it was by far the best volunteer experience that I have had. It is run by the people who work day to day on the project and this is really valuable to a volunteer placement. With other volunteer placements there is often little organisation and oversea agencies usually have no idea and no control about what is going on.
Santa Martha relies on its volunteers, and progress can be seen on a weekly basis. There is a real sense of direction and volunteers leave knowing that they have made a difference and that there work will not go to waste.
The Amazon location is a much pretty and nicer location to work, but the Quito location has the large animals and big cats, it is probably worth trying them both out, but a longer stay at the Amazon location is recommended.
The two sites have recently severed links with each other but are both still operating. Along the same road as the Amazon is the Arajuno Road Project, which works with schools and offers volunteer placements and has a similar volunteer ethic to Santa Martha. Here are the links for future reference.
Santa Martha (Quito) (animals):
http://www.santamartharescue.orgSanta Martha (Amazon) (animals):
http://://www.santamartharescue.org/amazonia.htmlArajuno Road Project (Amazon) (teaching):
http://www.youvolunteer.org