Had some trouble finding an answer to this, maybe I was wording it wrong. Here it is in case there is another curious party.

To change the shell that you use do the following:

  1. Click on the cog in the upper right of the GitHub gui
  2. Select Options
  3. Directly under Clone Path there is an option: Default Shell
  4. Select the shell you want to use when you go to start>git shell
  5. Click Save

Now when you select Git Shell from your start menu it will open Git Bash.