In Windows 3.1, the SYSTEM.INI had a setting called "shell" for overriding the default program started after Windows had loaded. Use of the word "shell" in this sense to describe a graphical interface dates back at least this far.
There was also a crude character-mode graphical interface called MS-DOS Shell, in 1988.
"shell" might be best generalised as "the first interactive program to run after boot" rather than "command line interface".