Mostly I use XLD (https://tmkk.undo.jp/xld/index_e.html) for audio conversion (as I'm mostly converting from .BIN + .CUE to "iTunes Plus" AAC for uploading to iTunes Match); but my understanding is that under the covers it's mostly just using afconvert (or whatever the system-framework equivalent of it is.)

So if your needs are just "one audio file in, one audio file out, and let me tell you exactly what it should look like", then afconvert is probably what you want.