Moorsan’s suggestion will not quote do what you want.
His idea is to close the current window and open a new one. While this will give you a window with no history, it will also kill any process that was going on in that window. For example, say you were ssh’d to a remote machine and you wanted to clear the history - this approach would close your ssh session and lose whatever you were doing at the time.
Unfortunately, though, there is no other obvious way of clearing the history. Terminal.app specifically marks the history of each window as being read-only, meaning a script can’t change it’s value. You can get the history, but you can’t clear it. About the closest you can get is UI scripting to change the window history buffer to a small value, then reset it, but that’s very clunky.