I do not have this problem on any of my three Lion Macs.
The difference in audio quality between your mics may simply be that your external mic is closer to your mouth than the one in your iMac. Sit as close to your iMac's mic as you can and record a short test wherein you speak louder to see if the audio auto-volume circuitry might be expecting a louder voice input.
If the loudest you are comfortable talking to your iMac does not improve your recorded audio, your iMac's built-in mic may have a problem. In this case, either have your Mac checked out by your Apple-Authorized Service Provider or use with the external mic whenever you need a good sound recording.