Try enabling “Audio Sync Enable” in the audio settings and enabling “VSync” in the video settings. Make sure “Video Driver” is set to “gl” in the Driver settings and Audio Driver is set to “xaudio”. With these settings enabled, if your monitor’s refresh rate is close to the core’s run speed (so, near 60 Hz), RetroArch should change the game speed and audio speed to imperceptibly match your monitor’s refresh rate and change the audio rate between frames accordingly, preventing crackles.
Please report whether it worked.
If this doesn’t work, it’s probably not a sync issue and it’s more likely related to the core. You can check out the core options by escaping to the quick menu which is the F1 key by default, I think. “Core Options” there should let you change some things.