You're right there seems to be is no reliable evidence that Thomas Middleton was a son of John Middleton, 1st Earl of Middleton.
The Scots Peerage, vol. 6, p. 185-186 has no such son, and the grandson of the first earl, John Middleton, titular 3rd Earl of Middleton, had no male heirs, which would be incorrect if Thomas was an uncle, given he appears to have descendants.
The Complete Peerage, 2nd ed., vol. 8, p. 697, also makes it clear that when John, 3rd Earl Middleton died, "the issue male of the grantee (John, 1st Earl Middleton) became extinct"
I've also added Scotland to the tags to this question, as that might be the most appropriate project.