"My mom had 2 boys, her mom had 3 boys"
Danny's statement was confusing but I assumed he was referring to Lindsay's mom with 3 sons. If he was talking about his grandma's sons or mom's brothers then he would say "my mom had 2 boys and 3 brothers." I think it's easier and clearer that way.
I do agree that it could be taken either way (he was talking about his own mom or Lindsay), but I've also usually assumed he was talking about Lindsay, because...well, genetics, and he's a scientist. Danny's maternal grandmother obviously had at least one girl along with those three boys, and if Lindsay has something like 3 sisters and zero brothers, or even if she's an only child -- it would hardly matter how many boys Danny's grandma had. It certainly wouldn't rule out the possibility of a girl.
...Of course, since Lucy turned out to be a girl, I have considered that maybe he
was talking about his grandmother and may not have taken Lindsay's family genetics into account.