Wash cranberries, discarding any that are not fresh and firm. Combine cranberries and apple juice in a non-reactive saucepan. Bring to a boil over medium-high heat, stirring often. Reduce heat, cover and simmer for 5 minutes (watch so it doesn't boil over) until cranberries pop. Stir often.
Remove cranberries from heat and puree until smooth. Press through a fine sieve and discard any seeds. Return mixture to saucepan and add maple syrup, honey, cinnamon and nutmeg. Simmer mixture uncovered for 10 to 15 minutes until desired thickness, stirring often. Remove cranberry butter from heat and stir in vanilla flavoring.
Ladle into hot 4 ounce or 8 ounce jars. Using a water bath process, process the jars for 10 minutes at sea level to 1,000 ft, 15 min at 1,000 ft to 3,000 ft.