When I was shopping for mine that is what my two options were. I decided to go with the one that would do what I needed and get better mileage. No doubt the 3.5 ecoboost is a much more powerful faster power plant and im going to say has had fewer growing pains than the ecodiesel, I just wasn't willing to give up the 30 mpg aspect.
Hope its a good one for you, I sometimes wonder if I made the right choice or not. My BIL bought a new 3.5 ecoboost the same week I bought my ecodiesel, they are both nice trucks.