Another way to do this by enabling the AppStore Debug menu.
Sign out of AppStore.
Open a terminal and execute the following command:
defaults write com.apple.appstore ShowDebugMenu -bool true
Open AppStore again and a Debug menu is now present.
Debug Menu -> Reset Application.
This will reset the current state of the AppStore, including current downloads. You will have to sign back in to see available downloads.
In my case I was able to stop the not yet finished download of XCode 4.0.1 in favor of just starting up the Xcode 4.1 download (since Lion only runs 4.1).
I wish I could have done Debug Menu -> Show Download Folder and just deleted the directory in com.apple.AppStore that was obviously 4.0.1 (based on size), but this didn't register in the AppStore. I wonder if the sqllite file in that same directory is where this status is stored.
If you are not comfortable leaving the debug menu enabled just run the above terminal command again, this time setting it to false.