I wait to clean ears and clip nails when Cruiser is sleepy. We usually wait until after dinner and play time outdoors and do it right before bed. The pb helps distract. Your approach is a big part of the process. Around 9 Cruiser flops down and wants to go to sleep, I usually will lay on the floor with him and rub his belly and give him a good scratching and once he is nice and relaxed I'll sneak in the pb and clean each ear one at a time. It helps if it is quiet when you are doing it, I've found background noise like tv and radios help add to the tension. You may want to use part of your training time to just rub his ears lightly with your fingers. Do it several times a day and try to make it fun. Give loads of praise and treats but don't do any cleaning when you do it. Make it a game. After a while, he will get used to you handling his ears and will be more receptive to cleaning. Also, you may want to look at what you are using, is it topical or does it go down into the ear canal. If there is alcohol in it, it may sting. There are quite a few cleansers that do not have alcohol that work well. I use a babywipe to clean the outter ear every few days if his ears are visabily dirty, and as I stated sometimes a little mineral oil on the outer ear area if scratched, and avoderm for the inner ear canal but only once a month. It goes in wet but dries quickly and causes the built up gunk to break apart.
I have an appaloosa that I rescued. He was extremely head shy and had been abused alot. When I first got him I could not touch any part of his face or head. He would lunge, bite, kick and throw anything that did. I ended up donning hockey gear and going in his stall while he ate and would rub him during every meal. I of course, ended up with a load of injuries, but now I can do pretty much anything I want with his head,ears and nose. Point is.. I invested time getting him used to having his head and ears handled and it payed off! I have had to do alot of desensitizing with my horses and have applied the practice to my other animals. Takes time but works!