It means so far, this is the best. However there may be better ones coming in the future. You can use it to scold people when the "one" is referring to excuses, lies etc. For example... "For all your lies, you think this is your best one yet? I know all your tricks for I have been there before. I can give you a better lie!"

Th expression "that's the best one yet" would not normally be used to scold or reprimand someone unless the speaker was sarcastic. The phrase would usually express someone's amazement at an accomplishment, the highest achievement thus far.