It's all about the individual...I've flown both the ERJ and the CRJ and have no preferance...I found both of them comfortable. It all depends on your size really.
I'm 5'8" so that might have a lot to do with it. Some people say that the ERJ is cramped but usually you'll hear this from someone who is 6' and taller. You'll also hear that the CRJ's window are kind of low, but not for me...once again maybe because og my height.
I found the ERJ-145/-135 comfortable.