No, it is not allowed anymore

All natioanl labs and other government employees are no longer allowed to write reference letters to support any one (including their own students or postdocs)'s green card case. Not even on their own plain letter paper. Of course, lots of bosses ignore this, but I also know lots of guys cannot get letter because of this. So it is based on his/her curtersy.

However, CIS can still check with him/her, so one way around is to cite this new rule and list the guy as a reference. Of course, before you do that, you need to communicate with the guy and make sure he is OK with it.