Is it possible your main window has been shrunk down a little so you can't see the machine control icon (it's happened to me and fooled me for a few seconds).
I have also just upgraded to Sierra and there is no Machine Control Panel. It is not that it is not in the Tools Menu, it is there but when it is selected no panel is opened. This same happens with the shortcut on the RHS and cmdP. Has anyone found a solution for this?