It's really tough. I was playing with this all throughout tonight's game (and over the whole season, really). All of our big-men are significantly floored. They defend different types of opposition to different extents (Thompson did really well on Giannis and was poor against Miami, for example), which makes it really difficult for me to state that one is definitively the best defender of the bunch.
Thompson is the best rebounder, Theis is the best at undervalued things like hedging, screening and hand-offs, and Timelord provides the best vertical threat we've had in years on both ends.
I'm not sure I even have an answer...