If you're looking for an alternative to Hiking the Inca trail, consider renting motorcycles and finding your own way there. Armed with a couple of local maps two 400cc bikes, my travel buddies and I drove over 8,000 foot snowy mountain peaks and down into sweltering jungle paths. The way there isn't always a road, and some improvisation will be necessary, but it's not a difficult ride overall.
Motorcycles can be rented in town (we had a good experience with http://www.ericadventures.com) and come with jackets, helmets and gloves. Accommodation can be found in towns along the way, and some hiking will be necessary to get into the site.