Is God Sovereign Over Disability?

Of course He is!  John Knight writes: 

"God's sovereignty doesn't mean he merely permits disability. . . .  [H]e sovereignly intends it, both for his glory and for our good." 

See this article on Desiring God blog for the full answer.  In this article, note his creative paraphrase of Psalm 139:13-16, with specific descriptions of disabilities.