I guess you rig is not helping at all, as you might know Crysis 3 is the game with the best graphics so far... Do you play another video game like Battlefield 2/3?? any game where you can compare the FPS ??
NyxSlayer has a good idea, try playing a few other games and see if they slow down as well, install a game on 1 harddrive and another game on another harddrive, you will find out if its a harddrive issue or a different issue.
temperature may have somthing to do with it, hardware will slow down almost to a pause if it gets really hot, which will effect game performace, rivatuner or MSI after burner are 2 free overclocking tools that come with an accurate temp monitor.