First of all, be sure to be logged as the user, whose Terminal history you wish to clear/modify.
The most basic way is the complete wipe with this command:
history -c
You could also delete an individual notation in history by doing this:
history -d PIN
(eg. history -d 1300)
(*Note, that the PIN is shown when you run 'history' in the Terminal. It is the number noted infront of the commands you ran, check picture bellow)
This will however leave a track. It will be recorded in history :)
If you wish to avoid that open the .bash_history file with an text editor and manually find&delete that damn line:
sudo gedit ~/.bash_history
Enjoy!