Though most tourists just head to Machu Picchu like a beacon, there are many other sites spread around the country, and many were built before the Incas rose to power. In the south, there are the Nazca Lines. Locals didn't seem to place much importance to them until Maria Reiche came to live there and worked tirelessly to preserve and promote the area. 183 km north of Lima are the ruins of the city of Caral. No other site has been found with such a diversity of monumental buildings or different ceremonial and administrative functions in the Americas as early as Caral. In the north part of the country, there are several important sites. In Trujillo, you can find the Temple of the Sun and Temple of the Moon pyramids. Just to the north of there, not far from Chiclayo, is the Tucume archeological complex that includes 26 mud-brick pyramids built in the 10th century. East of there, near Chachapoyas, is the mighty fortress of Kuelap (called "the Machu Picchu of the North") and a treasure trove of unexcavated or partially excavated ruins of cities.
Of course there are many other sites all over Peru that are important archeologically, but the ones mentioned are some of my favorites.
Though the sites in Colombia have not been as well documented over the years as Machu Piccchu has been, several are very impressive. Ciudad Perdida, which was built about 650 years before Machu Picchu, but was not discovered until 1972, is another mountaintop city hidden by the jungle. And recent lidar mapping of the area has revealed that the site is much more extensive than had been previously imagined. Much work is needed to reveal the vast area that lies hidden beneath the overgrowth. Further to the south lies the San Agustín Archaeological Park. This is the largest group of religious monuments and megalithic sculptures in South America. One of the early visitors to the site was a friar who saw the gods and mythical animals so skillfully represented that he thought they must have been created by demons because he didn't think that humans were capable of that kind of craftmanship. These 500 works of art, some as tall as 12 feet and weighing several tons, were created by a culture that flourished from the 1st to the 8th century. Nearby is the Tierradentro National Archaeological Park, which features a series of pre-Columbian underground tombs, known as hypogea, that are covered in indigenous art and reached by spiral staircases. The tombs date back between the 6th and 9th centuries AD. Recently, near San Jose del Guaviare, scientists discovered rock pictographs made by local indigenous cultures estimated to be around 20,000 years old.
Most people don't think about archeological sites when they think about Brazil, but there are certainly some there. The Serra da Capivara National Park is a treasure trove of archaeological and natural wonders. It's canyons hide some 500 natural shelters and caves, which have an incredible collection of paintings and engravings made by the men that inhabited the region. UNESCO has declared the park part of the “Cultural Heritage of Humanity“, due to the age of its archeological sites and the aesthetic quality of the rock art. Until recently it was difficult to get to the site because of it's remote location, but last year an airport was opened up nearby, so now it is much easier to get to there. Not well known and seldom visited is a mind-blowing archaeological site located at the headwaters of the Xingu River in the Amazon basin. In the Xingu region of the Amazon basin, there is an archaeological complex including twenty towns and villages, where close to 50,000 people may have once lived. It was likely inhabited from a period of time around 1,500 years ago to a time as recently as 400 years ago, when the people living there were likely killed by diseases brought over by Europeans.
The ancient site of Tiwanaku has long been known, but is still being investigated because there are nearby sites where not much work has been done. Recent research and lidar mapping have also revealed a vast ancient network of ruins in the Bolivian Amazon. Some of the inhabitants of this area are claimed to be of the Ese Eja group, so possibly some descendants are living across the border in Peru, where some members of that group serve as guides at Posada Amazonas and other lodges.