Could be a DoS or DDoS attack? Sometimes these attacks can cause a high CPU load if it isn't the plugins. Maybe it's just you're experiencing more traffic at certain times? Plus...since you're on a VPS, maybe another site hosted on the VPS is reaching traffic peaks or they're getting attacked and causing your site to lag or get high CPU load or both. If you're not getting attacked or are getting attacked, talk to your host about the problem and maybe they can help you block attacks and prevent them from happening again or move you to a different VPS if it isn't you being attacked.

Log into SSH and read this thread to see if you're being attacked and how to stop it:
http://www.besthostingforums.com/13-...ables-ssh.html