This is a hard choice, and it is sort of a false dichotomy, because the two are both heinous beyond belief. But I'll choose the Inquisition because, without a doubt, pedophile priests were common then too. The Inquisition was one of the most disgusting displays of human brutality in earth's history.
While the priests continue the heinous act of molesting the children under their care today, they aren't forcing adults to confess a sin they didn't do through torture, and killing them. During that time, they had control over everyone, and laws didn't apply to them. I have no doubt that they were still molesting kids during the Spanish Inquisition.
Both the Spanish Inquisition and pedophile priests amounted to torture sanctioned by the Catholic Church. The Spanish Inquisition was worse because it cost literal lives and those who perpetrated the inquisition got away with it. Pedophile priests have been brought to justice and the Catholic Church tried to make amends to victims of pedophilia, so that is at least better than killing innocent Jews in Spain.
I would say both the Spanish Inquisition and the pedophile priest problems are pretty big issues. When it comes right down to it I think the religious persecution is worse because more than likely these acts probably harmed more people total. I don't think that detracts from the idea that the pedophile priests are also a huge problem that has clearly caused many children problems. With all the things the Catholic Church has done wrong over the years, I fail to understand why so many people still favor it.
The actions taken within the Spanish Inquisition were horrific, without a doubt. However, things like that happened in many places that far back in history. In this day and age, especially in a first-world country, sexual abuse of minors is known by everyone to be wrong. The modern church needs to be realistic about the sexual needs of its clergy.
It is my opinion that the pedophile Catholic priests acted in a more heinous manner than the Spanish inquisition. The inquisition was based on religious principles, even though it was a carried out in a violent manner. The Catholic priests that became pedophiles had no moral, religious, or good reason to do what they did.