Albert Barnes Commentary Psalms 99:2

"Jehovah is great in Zion; And he is high above all the peoples." — Psalms 99:2 (ASV)

The Lord is great in Zion – Compare Psalms 95:3. The meaning here is not that God is “absolutely” great—which is indeed true—but that there is a sense in which he has shown himself great “in Zion;” that is, in his manifestations toward his own people. He has demonstrated power on their behalf; he has intervened for them in times of danger; he has so defeated their enemies as to show that he is a great God—a God worthy to be adored.

And he is high above all the people – Above all the nations. He has them under his control. He rules over all. The God who rules in Zion also rules all the nations of the earth; and his people, therefore, have special occasion to praise him.