It stands for Edward Jacob, because you know that Bella loves to make name combinations, like she did with Renesmee (Renée and Esme) combining her mom's name(Renée) and Edward's mom name(Esme).
What she was going to do with EJ, was to combine her love's name(Edward) and her best friend's name(Jacob), so it would've been a result of Edward Jacob Cullen.
As you may have understood it stands for Edward Jacob. But there`s something else I would like to comment-at that point Bella already knows she loves both Edward and Jacob.And she`s pretty much beyond that "he`s only my best friend" phrase-because what she feels towards Jake is madami than pure friendship. So what I want to say is that I thought it would have been completely inappropriate to name her and Edward`s child after Jake too, because that would have hurt Edward.And here I thought to myself-Gosh,how much madami selfish can Bella be!After all the times she made Edward feel bad-why is going on with this! So I guess it was a good thing Reneesme came in-she made everything right!