Really? What word would you use to describe a baby (or androgynous looking person) whose gender you weren't sure of?
I would certainly not used something like `is they a boy ?` though.
"Is it a boy or a girl?" or "Are they are a boy or a girl?"
Both are perfectly correct and common, but "it" sounds impersonal and as such can be a bit rude.
This is actually a problem for me. I can't see the difference between pink and blue baby clothes.