Question : How to properly query a domain for all DNS records

I've been using www.who.is, but it seems like it sometimes doesn't pull all the info, especially CNAMEs or A records

Any advice would be appreciated

Answer : How to properly query a domain for all DNS records

A tool like WHOIS from any provider can provide you with the DNS servers for a specific domain (NS records).  Once you know the name servers, you can query these directly.  If the DNS servers allow for a zone transfer, you'll be able to obtain all the records for the DNS zone.

In Windows, you could use:

nslookup
server x.x.x.x (where x.x.x.x matches one of the zones NS records)
set type=any
ls -d company.net
exit

If the zone does not allow for zone transfers, you could use a tool to enumerate DNS records like with FierceDNS (perl script):

http://carnal0wnage.blogspot.com/2007/12/fiercedns-for-dns-enumeration.html

Hope this helps...

Mike