I don't think it will make a gnat's butt worth of difference. Their ratings are too close. You'll get a few + plays because of their arms in CF, and a few less - plays because of their range.
Both will be great 3B, but that wasn't the question.
But I would play Gray in CF. He has the better bat and the way better durability. He can play everyday. Boyle needs to miss 30 starts, or so. Finding an adequate guy to platoon/switch off with Boyle at 3B will be a lot easier than finding one to platoon in CF.