For a milder purée, rub chiles between your palms to remove most of the seeds. Chop chiles coarsely with a knife or in a food processor. Put them in a bowl and pour the vinegar over. Cover and refrigerate overnight.
Add onion and garlic to the chiles and either cover the bowl with plastic and microwave on HIGH for 1 minute, or put them in a saucepan over medium-high heat, cover, and simmer for 3 minutes.
Let cool slightly, then purée in a blender until very smooth. Let cool.