We don't know - this is one of the unresolved LOST mysteries. There is some evidence supporting the 'Man in Black' theory:
- The whispers are strongly associated with the Man in Black.
- It explains why she isn't seen again - although there's a rather high mortality rate for Others, so she could have just died (and out-of-universe, it's likely that this was one of the loose ends that Cuse/Lindelof didn't have time to tie off).
- It explains her ability to appear/disappear.
- It explains away the problem with communicating with Ben, although given the presence of time travel and Ben's general conniving-ness, I don't feel it's possible to say that he couldn't have communicated with her.
- It gives her actions additional motivation - he's trying to use Juliet (like he uses others) to do something that would ultimately kill all of Jacob's candidates.
Her name (Harper Stanhope) is an anagram for "Perhaps an Other", like Ethan Rom's name is an anagram for "Other man". The "perhaps" is suggestive that she is something 'other' than a simple Other.
It's not totally clear, though. In The Official LOST Podcast (March 10, 2008), we find out:
CARLTON CUSE: Okay. Is this the last we've seen of Harper?
DAMON LINDELOF: No, she's an Other -
CARLTON CUSE: Might be around.
DAMON LINDELOF: She's still on the island. We didn't kill her.
DAMON LINDELOF: That being said, the podcast is not in canon.
DAMON LINDELOF: (laughing) No.
DAMON LINDELOF: So you should disregard everything we're saying.
CARLTON CUSE: Including what Damon just said.
DAMON LINDELOF: Including what I just said.
CARLTON CUSE: 'Cause he was just lying when he said disregard everything he said. That's a lie.
DAMON LINDELOF: Now this is like those two guys where one always tells the truth, and one always lies, and, you know, and you have to ask which one is guarding the gate to heaven and hell.
A couple of weeks later (March 28), there's this:
DAMON LINDELOF: They go onto a door that says "deceased"; once they die, we move them over there. And then there's the door that says "undead".
CARLTON CUSE: Yeah.
DAMON LINDELOF: And on the undead door there's only three pictures. One of them is...
CARLTON CUSE: Christian Shephard.
DAMON LINDELOF: One of them is Christian Shephard, one of them is Yemi, and the other one is...
CARLTON CUSE: Kate's horse.
Both "undead" Shephard and "undead" Yemi were the Man in Black (presumably also Kate's horse...), and at this point we didn't know about many of the other forms (Alex, Locke). If Harper was on the "undead" door, it seems like they would have said four, especially given that the episode was quite recent.