Ironically it looks like Nant-y-Maen gets it’s name from the nearby stream, which is itself named after the stone! Translating from the Welsh, nant means stream, and maen means stone. So the stream’s name means Stream of the Stone.
The nearby farm also has the name Nant-y-Maen, so it’s probable that this is the way it panned out...
1) The stream was named after the stone.
2) The farm was named after the stream.
3) The stone was named after the farm.
I suppose that the next logical step would be to rename the stream Nant-y-Nant-y-Maen.