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.
turn off background services from task manager,,,, And the most important thing .... When playing games, disable your antivirus temporarily.... Install Service Pack 1 .... update your drivers and try also updating your Bios...