Hi Lindee,
Does your niece sleep in the infant carrier to keep her at a more upright position because of spitting up? If this is the case, ask your sister to ask the pediatrician about getting a wedge for your niece to sleep on. It's a foamy wedge that sits perfect inside the crib and sits at a 45 degree angle (I think, can't remember exactly). The baby sleeps on it at an angle and helps with reflux and spitting up. My daughter had to sleep on one for the first few months of her life. She was an 8 week preemie but had a reflux as well as undeveloped pipes, so we had to add Simply Thick into her breastmilk for every feeding. Prior to us getting this wedge, you could hear our daughter "gurgling" and it was so disturbing and a couple of times she choked very bad. This was from her aspirating fluid into her lungs. We were lucky she happened to choke right when we were there with her or else no telling what could have happened. She slept much better with this wedge too. Have her ask for it. They cost $150 and most insurances don't cover it, but I can imagine sleeping in the infant carrier can't be comfortable at all for your niece - that could be a big reason why she wakes up fussy through the night too. I bet her back and bottom ache very bad.
In fact, we still have our wedge and I'd be willing to sell it for $50 if she wants to try it.
Good luck, she's lucky to have you for a sister!
-Char