goforit14

Since the journal gave you the choice, then it's really just your choice  
Also, keep in mind that despite our best intentions, the whole paper writing process might be slower than expected and by the time the paper is actually published, you would have started your PhD so when readers see your affiliation, it would be the correct one.
Personally, in your shoes, for now, I would just put the MA institution and if/when I become affiliated with the PhD school and use PhD school's resources to complete the manuscript, I would add the PhD institution as well. But again, this may be a field specific thing, where my field is not at all shy about having multiple affiliations per person. For amusement, here is a recent paper in my field, showing an extreme case (probably the highest density of affiliations to authors I've seen): http://arxiv.org/pdf/1604.03107v1.pdf
 

This may depend on the norms of your field so perhaps talk to your advisor.
In my field, I'd say that since you did this work completely while at your MA school (correct me if I'm wrong) so therefore you should just use your MA school affiliation. If you also continued this work while in your PhD program using resources at your PhD school, then students in my field would usually list both affiliations. However, it's not uncommon for students in my field to still only list their former affiliation if they did not use any resources of their PhD school to complete their paper (and especially if they worked on it only on their own time, i.e. not during the working time funded by their PhD school).
I don't think the email from your PhD school makes a difference in the affiliation listed on your paper.