he’s usually not there when I’m there.
I didn’t see this line.
Nonetheless, if you can wait until you see your boss again (i.e. it’s only a few days or so), it’s better to do it face to face.
Otherwise, send him an email saying that you need to schedule a face-to-face (or phone) meeting. It’s bad form to resign by email (unless, of course, it’s the ONLY way).
The Wolf