The feature request #874 is what you're seeking. Here is a summary of the feature request.

Ability to produce reports on Inbound and Outbound statistics for my internal domains.
For example - we own about 100 different domains which we are
authoritative for.
I would like to produce a report showing all of my domains and the total number of messages/recipients inbound and outbound.
In addition I would like to be able to produce peripheral stats as well
- Ironport anti-spam positive, Virus positive, etc for each domain.


You should bring this up with your Ironport sales representatives and let them know the value that it will bring to your company. Like if that feature was made available, you may purchase more machines.

Can someone tell me if there is currently the functionality to get mail flow reports on a per domain basis?

I mentioned it to our rep when we first installed the appliances and they said that it was a feature request, but I am not able to find any information on if this is available yet.