Quoting MahmuhMahmuh:" I have tried explaining to her the behavior problems I have with the older daughter, and she just yells ... [snip!] ... every time. I just don't know how to flat out say "I want to come get B, but I really can't take A with me this time".."
Ive had that issue with my sister and her two kids difference they are both blood related to me. It was a big deal for a while because her son is disabled and no one wanted to take him and do things with him so every time I wanted to take one of her kids she always made me take her son because I was the only one who would take him. I finally had to sit her down and explain to her that while I love spending time with just him I would also love to spend some one on one time with his sister. Your situation is a bit trickier but you just have to learn to stand your ground tell her that you want to spend some time with your niece offer to take both of them another time but tell her that once in a while you would like to take your niece and just do something with just her.