My microphone is not working in Safari, but works in all other apps. I can't even find the Safari audio input/output settings.
As a general rule, which sound input device is used is controlled by the OS in System Preferences > Sound > Input (as shown in the second image below) and some, but not all, apps one can choose a sound input device other than the one set for the OS. For example, in Audacity you can select other than the one set for the OS.
However, I am not aware of a built-in preference in Safari that lets one choose a sound input device. There is a microphone setting in Safari, but it doesn't offer control over which sound input device to use.
Have a look in: Safari > Preferences > Websites > Microphone