I'm not sure if she ever said she definitely preferred Jacob, I just don't know. I distinctly recall that she definitely gave a preference when asked whether or not she would want to be a werewolf or vampire, and she chose werewolf. I think it was because she simply couldn't envision eternity as a vampire, and the choice was so permanent. As a werewolf she could live as long as she wanted, but she would still have the choice of returning to a normal life. But, she has also described Edward as the ideal man and the "perfect boyfriend", albeit with some flaws that Bella eventually helps iron out.
In my opinion, though, I think she would have chosen Edward if he had been a human. She almost always describes Edward in more romantic terms, while referring to Jacob as the alternative pragmatic "choice". I don't think she could ever divorce their actual nature from their character, though, so while she might be drawn more to Edward, she would have chickened out and gone with Jacob. And I don't say that snidely, I think she took that question very seriously, and who wouldn't blanch at the thought of having to live through three days of burning in hell, breaking off all contact with your family and friends, and thirsting for blood and wanting to kill someone to quench that thirst. Take all of the ladies that love Edward and despise Jacob, and then actually present them with that choice along with all of the consequences, and likely a surprising number would choose Jacob.
But, SM the author never really has to make any choice, as she will always have both of them. I do think she will always have a very special place in her heart for Edward, the original superstar of her meadow dream. Jacob represents something else for her. I would be willing to bet she dove much, much further into Edward's head than any other character. She loved Edward's character, but he was causing her problems, and I think she was grateful to Jacob's character for coming into the story and helping resolve those problems. SM states in her interview from the guide that she was in Edward's head the entire time she was writing New Moon. Dang! That was a very dark place to be. I can see why Jacob's character was very attractive to her and gave her a freedom that she couldn't experience with Edward. My own theory is that a lot of the anger that is instilled in Jacob's character reflects SM's frustrations with Edward and the roadblocks his character keeps throwing down in SM's path. Hey, she is trying to get this story out, and you just END UP AND LEAVE! You are so going to get it.
If SM ever does continue the story of Jacob and Nessie, I expect she will have a lot more fun with Edward and Bella. Whatever initial draft she sketches out I would be willing to bet that E&B's role would become far more prominent by the time she actually wrote it down. As much fun as she had with Jacob, I think she would have a bigger blast with the new, unshackled, confident, bedroom-busting Edward.
P.S. If Stephenie could actually meet one of her characters and sit down and talk with them for an hour, who do you think she would choose, Edward or Jacob? I think she would love to talk to Jacob, but she would never be able to live with turning down a chance to meet Edward. Yeah, I think it would have to be Edward. Absolutely. I don't know what that proves, if anything, I'm just rambling here. But I think her heart would be going THUMP, THUMP, THUMP.
"It will take an amazing amount of control,” she mused. “More even than Carlisle has. He may be just strong enough…the only thing he’s not strong enough to do is stay away from her. That’s a lost cause.”