If you're jailbroken, iBlacklist is an excellent app. You can block SMS and calls from your phone completely. The app intercepts them, and can save the logs. It is password-protected, so there's an extra layer of security as well.
Even if you don't want to blacklist anyone, you can still set it so that you don't get a popup at all when new SMS messages arrive. Your messages will go to your regular inbox, and you'll still hear the alert, but no popup.
Free trial, costs $12 to buy.
I have also heard about MCleaner. Never used that one though.