Why did you single out my brother in law?
I am sorry I offended you. To answer your question, "why did I single out your brother in law," I turn to the original post:
"My sister has blue eyes and so does her husband. But her son has brown eyes and it's because one of her parents (my dad) had brown eyes."
The reason I "singled out" your brother-in-law is because he is the (genetically speaking, this is not a dispersion) merely the "alleged" father.
Biologically speaking, barring IVF egg switch, the woman KNOWS she is the mother. A man BELIEVES (with good reason) he is the father.
Yes, you mentioned four people (five by implication): sister, B-I-L, son, grandfather, and (by implication) grandmother.
Sister = bb (or, in my opinion, bB, being a Hazel)
BIL = bb (or possibly bB, being a Hazel)
Son = Bb (or maybe even BB, if Sister and BIL were Hazel)
Grandfather = BB or Bb --- both resulting in brown
Grandmother (by implication) = bb or bB
Now, your BIL is "singled out" because he's the only one who could be "in play." (The grandfather could, too, but it's not relevant --- again, talking biology here, not family dynamics.)
If sister was a bb and BIL was was bb, and the child was a Bb (brown), then something happened.
A "B" came from somewhere.
To quote the calculator above, the BIL is "likely excluded" from being the father.
Since you are sure of fidelity (and I have no reason to doubt), there are only a couple of things that could have occurred: (1) a one-in-a-million alignment of allels or MORE LIKELY (2) one or both of the parents --- probably your sister given your father's brown --- eyes is really a hazel, albeit a hazel that strongly favors blue.
That's it. Yes, it was flip and short (and hence this LONG post to prevent further misunderstanding), and for that I am sorry.
But the science is sound.
It is a very, very, unlikely event to get a brown-eyed son from two truely blue-eyed parents.