With the term "spirit", his reference is implicitly to electricity, which he apparently had some inkling of. Note that "spirits" in our vernacular refers to alcohol, which is the "spirit", or active principle, of wine.
At any rate, Newton was at pains explicitly to deny pantheism:
It is the dominion of a spiritual being which constitutes a God: a true, supreme, or imaginary dominion makes a true, supreme, or imaginary God. And from his true dominion it follows that the true God is a living, intelligent, and powerful Being; and from his other perfections, that he is supreme, or most perfect.
Here's the whole General Scholium. It's not very long.
Yes, the language of Newton’s time doesn’t always make sense to modern readers.
As I had said, he was a Unitarian who wrote numerous papers on religion and the occult, which would go against the idea of being a pantheist.