Can you replace a universal joint in a 2001 Honda CR-V or do you have to replace the whole drive shaft?

The U-joints can be replaced separately - you do NOT need to replace the entire shaft.

Thecvman on EBay sells the replacement u-joints for only $34. The original ones are made to be staked into the yoke ends, so you'll need to grind down the staked part (the little dimples that hold the caps in place) with a Drummel or abrasive roll cartridge. The replacement u-joint use "c" clips on the inside of the yoke so you won't need to re-stake them in place.