The question is "Why?". If you think you have a hard water scale problem, either might work, though I would try the vinegar first. It's cheap and safe for potable water systems. CLR is a poison and it says right on the package "DO NOT INGEST!". You would need to exercise extreme caution to flush it out after wards.
But there should be no need for any such treatment unless maybe you spend all your time in an extreme hard water region. Even then, the most likely problem areas will be faucets and check valves. And you will be well aware of it!
2004 American Tradition; 2014 Buick LaCRosse
Homebase in the Ocala Nat'l Forest near Ocala, FL