We actually just added this feature to Certbot. The only caveat is that you have to provide Certbot a script capable of configuring your DNS due to the large variety of ways this is done on different systems. Certbot sets environment variables to provide your script with the values necessary to complete the challenge. To do this, you need Certbot 0.10.0 and want to run a command like:
certbot certonly --manual --manual-auth-hook /path/to/your/script --preferred-challenges dns
You can learn more about this with certbot --help manual.