You are right, and your grammar checker is wrong!
In a sentence with a compound subject - in this case "the land, the seas, and sky" - the verb should be plural. And the clue you used, that this subject can be replaced by were, is a good one to use when checking for verb agreement.
Your grammar checker was probably fooled by the fact the noun right in front of the verb, sky, is a singular noun, and it was unable to see that the subject of your sentence is not just sky.
This is a good example of why we cannot depend on our grammar checkers in our digital devices: They make mistakes!