In Azure B2C is it possible to configure the multi-factor authentication to use the Microsoft Authenticator App?
At this time, Azure AD B2C does not support integration with the Microsoft Authenticator app.
You should request this via the Azure AD B2C forum in feedback.azure.com
This is now possible, albeit in preview.
See the Enable multifactor authentication in Azure Active Directory B2C official documentation and/or Thomas' answer below for more details.