Stir together lime juice and honey in a large bowl. Stir in pineapple and blueberries.
Spoon 1/4 cup yogurt into 6 (8-ounce) jars or glasses, and sprinkle each with 1/4 cup granola. Top each with 1/3 cup pineapple mixture. Add 1/4 cup yogurt to each glass, and sprinkle each with about 1 tablespoon pomegranate seeds. Cover and chill until ready to serve.