In a medium saucepan cook onions in enough boiling water to cover for 1 minute; drain and cool slightly. Remove stem ends; peel onions.
In a large bowl combine the 2 1/2 cups water and salt; add onions. Cover and chill for 4 hours; drain. Rinse with cold water; drain again.
In a medium stainless-steel, enamel, or nonstick heavy saucepan combine the 1 1/4 cups water, white vinegar, maple syrup, red wine vinegar, and juniper berries. Bring to boiling, stirring occasionally; reduce heat. Simmer, covered, for 15 minutes.
Pack onions into hot, sterilized half-pint canning jars, leaving a 1/4-inch headspace. Pour hot vinegar mixture over onions, distributing juniper berries evenly among jars and maintaining the 1/4-inch headspace. Wipe jar rims; adjust lids and screw bands.
Process filled jars in a boiling-water canner for 10 minutes (start timing when water returns to boiling). Remove jars from canner; cool on wire racks. Let stand at room temperature for 1 week before serving. Makes 4 half-pints.