What I would do:
--wash the eyes clean with saltwater (just water and table salt--any "saline solution" recipe from google should give reasonable proportions.)
--wash the eyes again if they get crusty again, up to two or three times each day.
--clean all the bedding and droppings out of the nestbox, and put in fresh bedding.
If it does not clear up in a few days, consider other ideas or talk to a vet. I have only seen a few cases of crusty eyes in bunnies, but every one of them cleared up just fine when treated this way.
I always left the bunny with the litter, except for the few minutes of time when I was actually washing the eyes.