You need to compare like for like. A typical bipolar technology now would be fairly large geometry and you wouldn't get many devices within a given area. The state of the art CMOS would be packing many times the number of devices in the same area so while it may be more expensive for a given area you have a lot more devices within that area. So, price per transistor is lower for CMOS. However, inherently the bipolar process is simpler - fewer masks and fewer process steps.
Keith.