By default iMovie doesn't recognize AirPods as a recording device. This probably has to do with Bluetooth latency or quality, etc. but if you want to force iMovie into using the AirPods as an audio in device you can do it by creating a new Aggregate Device with the Audio Midi Setup Tool.
First launch the Audio Midi Setup app, and click the + in the bottom left of the window. Select Create Aggregate Device
Next select your AirPods input device as the only device in the aggregate and name it something useful.
Finally, you'll be able to select your new Aggregate Device in the microphone selection dropdown in iMovie. Hope this helps somebody in my position in the future!