I wouldn't buy new unless the cost difference was negligible. Having said that, if that's what you prefer, and the shop is supplying the labor, then let them sort it out. They're the supposed experts.
If the plan is to buy through them and then install yourself, then i'd rethink the process. I would bet that one of the local auto part stores would have the alternator. On top of that, i think even though it would be rebuilt, it would have a lifetime warranty if bought from a place like Autozone.
03 Itasca Sunova, 8.1 Workhorse