As far as being with Eagle, I'd choose the ERJ definitely. More bases, routes, flexibility, etc. ERJs at all bases except SJU, with CRJs nice if you live in base but possibility of them switching bases like they did with DFW then you have to commute.
There's really not a huge difference between the ERJ and CRJ but if you talk to a lot of CRJ guys they act like their flying a 777 compared to the ERJ. Quote from a CRJ FO I jumpseated with once, "I would never want to fly the Embraer".