I was recently in Patagonia and Atacama, and there are many fine photography locations in both regions. Patagonia has many locations of interest to landscape photographers (lakes, waterfalls, mountains, pampas, etc), and is quite simply stunning. There are also a number of areas filled with water/shore birds of various kinds. Please note that Patagonia is quite large (Torres del Paine park alone is 500,000 acres), and the roads are poor. Unless you're into hiking/camping (which will restrict you to a relatively small area) you may want to use the services of the hotels that also offer guide services (you will be driven to most locations).
Puerto Natales and Punta Arenas are (relatively speaking) not all that far away, and in any case you have to pass through them to get to Patagonia. Punta Arenas is on the Straits of Magellan, and is one of the two hopping off points for boat cruises of Tierra del Fuego and Antartica (the other is in Argentina). I haven't been there myself, but there's penguin colonies in the area.
Summer in Patagonia, especially in the hills, can be something other than what you might expect if you're not familiar with mountain weather. As they say, the weather is variable, meaning every 15 minutes or so. Snow is not uncommon in the hills even in the middle of summer. Summer is also the windy season, and in exposed places (eg hilltos) you may have difficulty even standing upright, let alone getting some good photos.
Atacama (San Pedro area) has some very unique desert landscapes, along with small geysers in the mountains, a couple oasis, and a salt-covered lake with flamingos. Lots of guide services (some better than others) are available to take you to the unique spots. Due to the desert heat, many activities are arranged early in the morning or late in the afternoon, and are often of a few hours duration rather than all day hikes.
Chile is a very friendly country, with few problems of crime, institutional corruption, etc. Can't speak for Peru as I've never been there.
Let me know if I can hekp further.