Yes if a full rebuild is being done the gear set is off or partially off so the cost is little...just time to properly set up the depth of the new gear set.
To have the Gears swapped you'll be in the $200-250 for labor, plus gears $179-$200 and I would supply them a "gear set-up kit" so you have all new bearings, etc.. $100. It's a good time to install new axle bearings and seals if you have any issues or leaks. I personally install and recommend the Motive or Pro5.0 gears (made by Motive), or the Ford Racing are my second choice.
I have found some other guys just swap in gears using the same shims that were in the stock housing, while this may work it is not the proper way to do them. The new gear set must be measured and set up all new, this will ensure a long, quiet rear for many years.