I haven't tried it myself, so I may be missing a step. Assuming you're using the standard NSClient++ configuration, you'll have to modify the check_nt command in commands.cfg or add a new one. The default one defines port 12489. You can change it to not specify the port and then you'd define it in the service check definition or you can add another command definition, one for each additional port.
My command definition looks like:
command_line $USER1$/check_nt -H $HOSTADDRESS$ -p 12489 -v $ARG1$ $ARG2$
Maybe you'd add another that looks like this:
command_line $USER1$/check_nt -H $HOSTADDRESS$ -p 12490 -v $ARG1$ $ARG2$
The corresponding service check would then look something like:
service_description Net Logon
check_command check_nt_p12490!SERVICESTATE!-d SHOWALL -l 'Netlogon'
You'll need to open up that port on firewalls and whatnot, obviously. Then, on the client, you'd modify the NSC.ini on some_machine and just change the port= line to 12490. If you have loads of other ports you'll be adding, it'd probably be cleaner to leave the port out of the command definition and stick it in the service defintion instead.
As mentioned, I haven't tried this myself. Proceed with caution.