I haven't read comments like this before; I was a bit surprised a magazine for brides chose the Machu Picchu Sanctuary Lodge as the second best hotel in this continent for a honeymoon
. Anyway I guess it depends on interests of each couple. I think Cusco and Machu Picchu would be a great place for a honeymoon if you love history, mystical, and nature.
In the election participated some 7,000 travel agents. I couldn't find the article in the brides.com website, but it's in several peruvian news websites. The first place went to Four Seasons in Península Papagayo, Costa Rica
http://news.machupicchu.com.pe/node/501