mdchick- congratulations on starting and sticking to a pretty substantial new cardio routine!!! Keep at it!!
That being said, using the elliptical and running are not the same thing. Its like asking which is better, riding a bike or walk/jogging......Running uses completely different muscles then the elliptical. Even if you can go 3 miles on the eliiptical you might not even be able to run 1/4 mile, at least right off the bat. No one person can say which is "better" for you though. do what you enjoy, and whatever exercise will keep you motivated!