Actually some unix distros allow you to specify the port for DNS in the /etc/resolv.conf nameservers entry but unfortunately Ubuntu isn't one of them. If it were possible you would specify the DNS port in /etc/network/interfaces along with the IP address of the nameserver — presumably a loopback address in your case.
There is an enhancement logged: Please allow specification of port in resolv.conf
My guess is that you will have move the port that your VPN is using. However, there is probably a good reason why the VPN is listening on the DNS port. You might want to check it out before trying to change it; you might be trying to do something that it already does for you.