When a user looks up "mysite.com" they are going to get a single IP address, and there is no way via DNS to return different IP addresses based on the port number you are trying to use. You have a couple options to achieve this solution:
- Setup an intermediate routing service that accepts all traffic to mysite.com and then routes the traffic to the appropriate website/VM based on the port number. This is non-trivial and may incur extra costs (you could build the routing service into the existing VM that is serving FTP to reduce the cost).
- The easier solution is probably to have a CNAME for www.mysite.com pointing to the website, and a CNAME for ftp.mysite.com pointing to the VM.