If i am liked by the NCR and i decide to nuke them at the end of LR to get that oh so beautiful PA what will my rep be with them?

If you're "Liked" by the NCR when you nuke them, your reputation will change to "Soft-Hearted Devil" and they'll be hostile to you.

So you want to wait until you're "Idolized" by the NCR before you nuke them. You will then become a "Wild Child", which is a neutral reputation.