I went through the Mayuc Company based out of Cuzco for a Apurimac and Urubamba river trips. I loved the apurimac!
I know of a few places that are pretty sweet and you should check out. I'll break it down by region.
North: The northern most tip is where Hemingway stayed, a lot, and got inspiration for some of his stories. The waves come across the coast in the opposite of normal direction, and in one area you can catch a wave for something like a mile. In the city of Trujillo (The city of eternal spring as the locals call it) there is a lot of culture from the Incas. You can get to Huaraz, and soak in treks and views of the Cordillera Blanca section of the Andes. For a pic of some of the more well known peaks
http://www.summitpost.org/siula-grande-and-yerupaj/923380.
Lima: There is a lot to check out as far as Incan culture and history. The city itself is very, very dirty. A little further south you can go down and hike close to the Nazca Lines, or do a fly over.
Cuzco: There is the Salkantay trail, something like 5 or 6 days that takes you into Cuzco. There are so many other trails that you can trek and get to Machu Picchu the back way. There is a ton of cultural sites to see in and around Cuzco as well. If you go down the train tracks in Aguas Calientes, which is at the base of Machu Picchu, you can climb the trail to the top of Putukusi. It's a cool view of the old city and you get there by hand made ladders and a moderately tough trail. (when I did it, it was just me a one other person.) I would suggest to anyone going to Machu Picchu to visit twice. The first time take the tour and get the history and the whole story then you can wonder around through the city. Then go and hike Huayna Picchu which is a relatively exposed trail, much like Angel's Landing, to the best view of the old city. My favorite view of the city and the surrounding mountains is from the top of mount Machu Picchu. The trail is old and not maintained and totally awesome.
South: Colca Canyon outside of Arequipa is awesome. You can climb Mount Misti or any number of old volcanoes. Lake Titicaca is beautiful and you can take a tour with the Uru people who live on reed islands and float around on a boat made of reeds.
Jungle: Go to Iquitos, the head of the Amazon river and take a boat tour, or get back into the jungle. I'm not sure if they do this or not anymore but swinging on vines is not overrated. Take a tour into the Manu National rain forest and spend days with Macaws and other jungle life.
I don't know of any other travel agencies or the like. I made things up as I was there. I served a mission in the jungle and then spent over a month in and around cuzco doing research. I am jealous and excited for you. I hope this is helpful.
Salud!
