@Jmw2owl,
Your description of the situation does make it sound like at least one of them is depressed. Where are the children while they're both at work? Does someone care for them?
As your niece is 3, they should be preparing her for pre-school/junior kindergarten. In a lot of jurisdictions, children will not be accepted for pre-school/jk if they are not toilet trained.
Maybe you could try having light conversation about how exciting it is that your niece will be going to school soon - ask where she'll be going - have they visited the school yet - made plans for schedule changes when school starts etc etc . Obviously not all of the questions at once
Is there any way you can go out for a walk/park visit with your sister/niece/nephew when you visit? Even a visit to the McDonald's or Ikea play areas could help if they're around. Being outside of the home might help her frame of mind.