|MadSci Network: Zoology|
You can, of course, call an eagle's nest a nest. The word I think you are looking for, though is aerie. The word aerie can refer to any nest that is built on a high place, usually a cliff, but it is commonly used to denote an eagle's nest, as in an eagle's aerie. The word aerie itself comes from the Latin area - open space or threshing floor.
I hope that helps!
Try the links in the MadSci Library for more information on Zoology.