There is, as far as I know, no standard/method that allows a user to select which MFA they want to use to login with from the commandline prompt during login. (But you could always write your own PAM module to do so ... #CurrentTeam did but didn't release that to the public domain.)
Not the most transparent for end-users, but something you can do with stock tools is to use PAM chaining to configure a fallback method.
Set the Yubico PAM module as
sufficient and when you pass a valid One-Time-Password (OTP) you'll be granted access.
When what you entered does not validate as a correct Yubikey OTP, then authentication will fall through to the next allowed method, the Google-Authenticator PAM module.
That PAM module should be set to
If you then, after failing to enter a valid Yubibey OTP, enter a valid Google Authenticator code, you will be granted access and otherwise if you don't your authentication will be rejected.
That should somewhat similar to adding the following:
auth sufficient pam_yubico.so id=16 debug authfile=/path/to/mapping/file
auth required pam_google_authenticator.so