If I want to thank someone because mntioned a good subject, which one would be the best and why?
- Thanks for pointig great note.
- Thanks for noting great point.
Or are these basically the same?
I would say, "thanks for making a great point." Neither option you mention seems appropriate.
You also need the indefinite article before great: "Thanks for making great point" would only be said by a non-native speaker.
"Pointing a note" does not make much sense. "Noting a point" is understandable, but I would recommend saying, "making a point."