You don't really want to bring it to a full boil, but keep the water temp just below. Submerge the skull for about an hour then start scraping. Get as much as you can off then stick it back into the water for about 15-20 minutes before pulling it out to scrape again. Keep doing this until the skull is clean inside and out. The hard part is the brain and all the gunk inside all the crevices.
One thing, DON'T OVER BOIL. The skull bones will start to separate if you do. If that happens you can repair it, but why go through this if you don't have to.