Yes, The Last Temptation of Christ was hugely controversial. The sequence you refer to is essentially all in Jesus's head - speculating on a final temptation, so to speak, before he goes ahead, lays down his life, and thus fulfils God's plan of salvation for mankind. I understand why some Christians took against it to a point, but in the end, Jesus is still clearly divine, with a mission, and he fulfils that mission. Not one of my favourite Scorsese films, but an interesting watch.
Pretty Baby is pretty contentious. Leaving aside the naked twelve-year-old girl in sexualised context issue, I don't think its a great film. Louis Malle has made much better pictures (Lift to the Scaffold and Au Revoir Les Enfants, for instance).
Taxi Driver is a masterpiece. I could have included that on this list, for sure.