Yes he is. He tells us so in Scripture:
Then the Lord said to (Moses), "Who has made man's mouth? Who makes him mute, or deaf, or seeing, or blind? Is it not I, the Lord?" (Exodus 4:11)
As he passed by, he saw a man blind from birth. And his disciples asked him, "Rabbi, who sinned, this man or his parents, that he was born blind?" Jesus answered, "It was not that this man sinned, or his parents, but that the works of God might be displayed in him." (John 9:1-3)
To be clear, God's sovereignty doesn't mean he merely permits disability. These verses show us that he sovereignly intends it, both for his glory and for our good—"that the works of God might be displayed."
With that in mind, what do you think about this expansion of Psalm 139:13-16? I've added some additional descriptors in italics to bring out what we really mean if we believe that God is sovereign over disability:
For you formed my inward parts with Down syndrome;
you knitted me together in my mother's womb without eyes.
I praise you, for I am fearfully and wonderfully made with cognitive challenges.
Wonderful are your works in creating me without limbs;
my soul knows it very well though my ears will never hear a sound.
My frame was not hidden from you as you made me with Apert syndrome,
when I was being made in secret with autism,
intricately woven in the depths of the earth without Hexosaminidase A.
Your eyes saw my unformed substance with spina bifida;
in your book were written, every one of them,
the days that were formed for me with cerebral palsy,
when as yet there was none of them.
* * *
For more biblical and visual proof that God is sovereign and good in designing disability, check out Krista Horning's new book Just the Way I Am.