I don't think those should by synonyms.
"Command line" is often contrasted with a GUI; it means that you're typing commands in a terminal-like Window. It's a platform-agnostic term, used in Unix-based and Windows-based systems (and probably others).
"Command prompt" is the name of Windows's command-line interface ("terminal"). I've never heard it used for a non-Windows-based system.
I propose that they be somehow unlinked.