There are many choices… you have to match the flavor of sound that pleases you as well as pick and choose the very best. So, are you spending the same on both? So $5K on mid-tier 3 way or $5K on a high end 2 way?
Assuming careful choice then under these circumstances I would expect the three way to outperform.
But if we are talking about a $2K 3 way and a $5K or more two way… then the 2 way will outperform… it will sound tighter, image better and have a much better cabinet design. It will contain much more design thought and better components. I have heard some breathtaking 2 way high end speakers… leaving nothing wanting.