should I replace one or both and how much should ti cost?
Honda CV shaft replacement on 1999 Honda Civic
Go to http://repairpal.com/honda-civic-1999 and put in your info and if only one CV Shaft is bad no use replacing both.
Since the drive axles parts are expensive it makes sense to only do what's needed. It might be a good time to check the CV boots to make sure that they are in good shape. If there are any cracks or leaks you should replace them.