It depends on what airline you are flying and whether or not you are taking the Magical Express.
If you are taking the Magical Express and flying on one of the participating airlines, then you will need to visit the resort airline check in desk at your resort to get your boarding passes printed.
If you are not taking the Magical Express or flying one of the participating airlines, then you can get your boarding passes printed at Guest Relations at any of the theme parks or your resort's lobby concierge.