By default, all Canvas Course are created with hidden links  for My Media and Media. Unlike Canvas links, when hidden, Third Party Links do not show up grayed out in the navigation bar. To unhide, click Settings > Navigation, and drag up the links to unhid them. Be sure to click Save. You may need to scroll down to the bottom to find it. Please Do Not try to add these tool as an External Tool in a Page.  

Note: If you need access to My Media, but want the link hidden in the course, the My Media link can be accessed by going to Account > Settings and clicking My Media.