Here's a link to some home remedies.
http://lowchensaustralia.com/health/eareyes.htm#mites
These home treatments can take up to six weeks. It's not unusual for the puppy to develop an ear infection with untreated mites and that may be what is actually bothering him so you would need an antibiotic (prescribed or natural). I don't know if you have ever had an ear infection, but they are extremely painful.