Being messy is one thing, being unsanitary is another and is unhealthy, can cause sickness, and can be embarrassing to children when inviting their friends home. If unsanitary conditions are what concerns you, you may want to point this out with examples of what can happen. If it's just clutter, I wouldn't say anything. Sometimes there are more important things in life. Are the children shown lots of love? Do the parents spend quality time with their children? Are the children well-fed and clothed properly, and how is their hygiene?
Your concern is real, but you risk your relationship if you say anything. I would first consider how dangerous the situation is. Kids are resilient. It would be nice if everything were perfect as you see perfect, but not everyone is the same.
Perhaps time spent with your nieces and nephews would be more meaningful if you saw them outside of their house -- invite them to visit you or meet somewhere like a park.
Whatever your decision, I wish you the best. You can be a big influence on these kids.