They both mean the same thing but the second one might suggest that the person is being a bit sly. That they are implying something negative rather than saying it directly. The first one could mean this too, or it could just mean what the person is saying is unclear.

I think the difference is in the ‘mood’ rather than the meaning. ‘What’s your point ?’ is quite terse, impatient, as though the listener has heard you ‘rambling on’ i e talking a lot about something but you haven’t made clear what you are getting at. The second question "What are you getting at"? is neutral in mood, and doesn’t imply the same frustration or impatience as "What's your point ?"