Have you set up forwarders on each DNS so that it know where to forward queries to the other domain?
E.g. In on dns.domain1.com on the DNS console, right click the server ? Properties > Forwarders. Add the other domain DNS name, e.g. domain2.com and specify the IP address of the DNS server in domain2.com. (and visa versa on the other server).
If you're still having problems, like gtworek says, check that port 53 is not being blocked. Try this -
From the DNS server in domain1, try the command:
telnet [IP of DNS server in domain2] 53 (example : telnet 192.168.0.10 53)
If you get a blank screen appear then the port is open. If you get an 'connection failed' message and no blank screen then port is being blocked.