I would contact her doc. I wasn't aware of her ng tube; I wonder if that is dulling her ability to swallow/respond appropriately to the mucus, and allowing her to choke on it more. I also wonder if the tube is irritating her nasal passages and actually causing the drainage in the first place. Is she receiving pumped breastmilk, or formula, or what? If she is receiving something other than breastmilk, depending upon her age, the doc might want to add more water/clear liquids to her intake, to increase her hydration.
If I ever have a true concern like this, I don't hesitate to call the doc. That's why they earn their money...it's their job. And you aren't the reason they didn't get a good night's sleep. I used to work at the hospital overnights; we were always paging the on-call docs. So, even if you end up calling at three am, I'll bet 10 other parents and many more nurses have already called with questions and concerns.
Keep us posted on how she's doing!