"Per"="for", so it makes no sense to say it twice. How much do you charge per unit? How much do you charge for each unit?

How much do you charge per unit?

Its correct to say "How much do your charge per unit?" but people don't really speak like this. This is an exact translation from a Chinese sentence like 一个多少钱/多少钱一个？(How much each?) The measure word 个 literally means "a unit" of something. Say: "How much are they each?" Or state the object in the sentence like 报纸一分多少钱？ "How much are the newspapers each?" You can also say "How much do you charge for one?"