You can help your pup get used to having you touch his face by touching him often when you give him affection. Rub the hair down on each side of his nose, stroke his forhead, chin and do lots of touching and soon he won't mind you touching his face to clean it.
I use clean cloths, water and if it is really bad a drop of baby shampoo. If you get the crusties wet first, they will soften up and come out much easier.
LuLu drinks from the bottom of her water bowl, and she gets her beard in her food so she gets her face washed after eating.
The more often that you do it, the sooner that your pup will get used to it.