I have been to both, personally the funnest flying I have had was with eagle but that was a long time ago, in MIA. The company is stable, animosity with mainline but which regional isn't with their partner. Longer upgrades but again, experience and stability for what its worth.
As for Comair, I highly discourage anyone from coming here right now. LOTS AND LOTS of attrition, now that may mean quicker upgrade than eagle but domiciles are horrible...JFK you will go, and changes too many to name here. Many good pilots with great seniority leaving by the ten fold giving up lots and a pretty good salary. That is a clue to the conditions here right now. These conditions have existed for quite some time and will continue for quite some time. Eagle, you have LAX (although senior i am sure) DFW ORD MIA and I think BOS not certain and of course "The Rock" In my opnion, for state of mind, I would highly recommend Eagle. Thats just me.