Muriatic acid is what brick masons use to clean iron stains and calcium/limestone deposits from brickwork and other masonry. It is available at hardware stores.
I have used it to clean mineral specimens, but be careful what you choose to clean. Clumps of quartz crystals can fall apart during the process. It wont hurt the crystals themselves though, but it could mess up a nice looking specimen.
I got a heavy plastic bucket with a lid and put it outside in a safe place away from pets and kids. I just kept checking it to see how it was working and when I was happy with the outcome I put it in a pail of water to neutralize the acid. This is when I found out about distilled water. My first specimen was rinsed in regular tap water and the iron in the water gave the quartz crystals an orange tint. So I switched to distilled water and they came out clean.
Good luck