This is surprising if you're running the script in one window and trying to get work done in another! The AppleScript answer given in this thread works, but it has the nasty side effect of clearing any terminal window that happens to be active.
See Chris Page's answer to How do I reset the scrollback in the terminal via a shell command? for more information. Which clears the scrollback buffer as well as the screen. Or more concisely ( hat tip to user qiuyi): printf '\33c\e[3J' If you're using the OS X Terminal app (as stated by the OP), a better approach (thanks to Chris Page's answer to How do I reset the scrollback in the terminal via a shell command?) is just this: clear & printf '\e[3J' A better way to clear the screen from within a script.
