I have to say I liked Boneshaker better, but only just a little bit. And I didn't love either one of them. I had problems with the endings in each and similar problems with character in each...that being that I hated one of the POV characters in each. With a passion. To the point that those chapters detracted from my pleasure in the story.
I hated Zeke in the Boneshaker, and I hated the Jaidee/Kanya pair in The Windup Girl.
I also felt that the ending was the weakest part of each novel...Boneshaker kind of dribbled off at the end, for me and The Windup Girl...well, lets just say that my sense of justice is offended by The Windup Girl's ending. Kind of like it was by Babe 2: Pig in the CIty. I felt appropriate come uppances were missing and the supposed good that was to come to my favorite character (who was, in fact, the only innocent in the story) was going to be just as bad as all the other options, given who it was being offered by.
Now, I liked great chunks of both books. The first 22 or 23 chapters of The Windup Girl were some of the most compelling writing I've found in a while. It kept me well gripped. I just wish, in both cases, that the endings had been more satisfying to me.