I think they're both fine. But I'd go for Emma here, since the reboot is rumored to concentrate on the high school part a la Ultimate Spider-man. MJ doesn't have to be a supermodel type yet, just the girl-next-door type who likes to party and a contrast to sweet Gwen.
Oh, and for the record, I liked Kirsten as MJ. She did what she was asked of the material, manfeet or otherwise.