afcovert uses the superior inbuilt AAC converter. FFmpeg can do this as well with the right arguments but you have to dig them up and the quality is capped to a lower value than you can get with afconvert.

ffmpeg offers a few different encoders for many of its supported audio/video formats, and the result depends on what encoder you tell ffmpeg to use. It does not have support for using Core Audio on macOS but it does offer FDK AAC, which is one of the better AAC encoders available today - though not nearly as good as the one available in Core Audio.