My guess is Harry. I got there through process of elimination.
Both Mary and Phin seem like obvious choices to me. Mary's been circling the drain now for a couple of books. Kork killing Mary is just too easy. Phin's also been dying of cancer for what seems like forever. In both cases, I think it makes more sense --- from a story standpoint --- for those characters to die naturally. Besides, Phin is Joe's Repairman Jack and he's just too cool. (BTW, Joe, I'd pay double the cover price for a Phin stand alone.

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At first I thought it was Herb. But it didn't make sense that the captain would offer to help with funeral arrangements if it was Herb because, you know, Herb's got a wife. The only way this makes sense is if Herb's wife is in the hospital and that isn't the case IIRC (sorry... I can't refer to my copy because I just loaned it to a friend).
I ruled out Latham because, while he's important to Jack, he's really just a walk-on. Not exactly a redshirt, but I don't see him as a beloved character among readers. One of the fiction writing rules is "Kill a beloved character." Latham just doesn't fit that profile. If he died, it'd affect Jack to be sure... but I don't see his death affecting readers on a wide scale.
The last to consider is Jack. Again, I don't have my copy of the book and I don't remember whether the last chapter had a POV tag. Absent that verification, I waver on this because what better way is there to shock your readership than killing a series main character (THE main character in this case). It's risky, but not outside the scope of possibility. Then again, Kork's nemesis --- the Batman to her Joker --- is Jack. The payoff of just doesn't fit the end if Kork is sending someone else to "Come get me" note.
Of course, all my sturm und drang over whether it's Jack could be hokum if someone can confirm whose POV is on the last chapter. If it's Jack, then that leaves... Harry.