External hard drive problems
Sure this problem applies for both your drives? Could be that one drive affect the other thru your USB controller. Try to disconnect one of them and see it it gets better. If it doesent, swap them to see. If it gets better while one of them is disconnected I would limit the problem to be a faulty drive. 

You could also try to check if some processes are accessing your drive. Have you checked torrent or so aren't loading to the drive(s)?

Alternatively you could turn off the option for spinning down your hard drives when possible in your settings panel for power.