Poor boy! I don't know if I have any advice. Kenya is prone to ear infections, but they itch so she LOVES it when we rub her ears and scratch them. She likes having the ear drops put in because then I have to rub the base of her ears to work it down and she likes that, then she gets a dog biscuit.
The problem with a muzzle is it can freak out a dog even more. Coke got a big, nasty hot spot pop up on Sunday morning and even being muzzled and tethered, I could not get near it. The muzzle makes him even more stressed and he panics.
Someone on another board told me she learned to restrain a dog by lying the dog on one side and then putting pressure on the elbow that's against the ground because the dog needs that leg to get back up. I guess you could do that, one side at a time.
Also, could the drops be cold? Kenya will sometimes flinch if her ear meds are cold. You could rub the bottle in your hands, or hold it in some hot water first so it's more body temperature. I know I wouldn't want something even room temperature in my ears!