You need the tool tfs.exe, which is installed togetcher with Visual Studio. You can start a Visual Studio Command Prompt. I tested the procedure below on Visual Studio 2008 and Visual Studio 2010.
In the commands below, replace serveraddress with your TFS http or https address, e.g. https://tfs.mycompany.com:8443. You can find it in Visual Studio: menu "Team", menu-item "Connect to Team Foundation Server...", button "Servers..."
The existing workspaces for some "computername" can be queried with this TFS command:
You get a list of all workspaces, with the existing mappings. It is the workspace name (behind "Workspace:") and the owner that you need in order to delete the workspace.tf.exe workspaces /computer:computername /owner:* /format:detailed /server:serveraddress
Now run this TFS command to remove the workspace "workspacename" for owner "owner":
tf.exe workspace /delete workspacename;owner /server:serveraddress
Please be aware that the workspacename and the computername can be different. On my machine, the first workspacename was the same as the computername, the next workspaces were suffixed with _0, _1, ...