I recently reconnected to a TFS 2013.3 Team Project after quite a while away. I knew that additional Git repos had been added to the team project, but Visual Studio 2013.3 was not displaying them in Team Explorer. It turns out that you need to click the Refresh button (see the red rectangle, below) to update the list of Git repos. Once you do this, you can see (and thus clone) any of the existing repos.
HTH
Rob
This post was migrated from https://blogs.msdn.microsoft.com/rob/2014/10/27/viewing-all-of-the-git-repositories-in-your-tfs-team-project-within-visual-studio-2013-3/.