The condom makes the act non-reproductive in type, whereas NFP does not. That the consequence is the same (that in each case, the couple does not conceive) does not make the moral status of the act the same.
To put it a bit more crudely in a more extreme example, it would also be non-reproductive in type for a couple to watch porn, masturbate, and then “complete” the act together. Here the couple might conceive as they would in natural sex, but the moral status is not the same in any case.
You are interfering with an act that must be procreative whether its consequence is procreation or not. (For that reason, a couple practicing NFP must still be open to children. By practicing NFP, one should not be conceiving of oneself as blocking procreation.)
Intention is not simply about what one professes to aim at. By virtue of undertaking certain acts we undertake a certain intent, whether we profess that intention or not. Contraceptive sex essentially avoids procreation.
This distinction is made elsewhere in Catholic moral theology. Craniotomies (where a child’s head must be crushed to get it through the birth canal) cannot be performed, even when the mother’s health is at risk. This is because it is impossible to crush the child’s head without intending to crush the child’s head; even if I say I am just trying to save the mother, I can’t separate my action from the intent to kill an innocent child. By contrast, the removal of a cancerous uterus can in some cases be morally permissible for the sake of the mother’s life, even if it is foreseen that it will result in the death of the child, because the act of removing the uterus can be sufficiently separated from the intention to kill the child.
Sorting out intentions can be difficult. There are cases on a number of issues where two acts can have the same consequences, but one of the two cannot be performed without an evil intent.