“Then, in the very last paragraph, he begins, “And now we might add something concerning a cerain most subtle spirit which pervades and lies hid in all gross bodies.” Speculating that, “... animal bodies move at the command of the will, namely by the vibrations of this spirit, mutually propagated along the solid filaments of the nerves, from the outward organs of sense to the brain, and from the brain to the muscles.”
Well, that’s more-or-less expressing a belief in pantheism (ie. that the universe itself is God). This sort of thinking is common among men of science. Einstein was a pantheist, as was Carl Sagan, and also Stephen Hawking.
Newton considered himself a Unitarian (a Christian who does not believe in the Holy Trinity or the divinity of Jesus) and wrote extensively on religion and the occult.
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.