There are so many things to address here. First of all, your niece lives in NY and you live in Florida, so my first question is this: How long has it been since she has seen you? How often does she see you? My niece is five years old as well and can be fickle sometimes. VERY fickle. She will visit me at work one time and hide behind me, refusing to speak to any of my coworkers. The next week she will come and talk their ear off. It's often just a matter of exercising control over her situation in anyway she can.
You also slipped something in at the very last sentence, more as a woe is me statement when in reality it could be a legitimate reason she was wary of you. Coupled with the fact that she does not live near you - you said you are handicapped. In what capacity? I remember when I was seven and my cousin who was about 11 years old at the time, cut the tip of her finger off (a door slammed on her hand, SO MUCH BLOOD!!!). I was there when it happened, so that alone was traumatic for me. But the point is that when they put an enormous bandage on her hand, I wouldn't go near her. Even though I knew my cousin very well, I saw her every single day - the bandage was enough for me to not want to be around her.
If your niece doesn't see you often and you are in a wheelchair, or use crutches to get around with, it just may be more than her five year old mind can comprehend. The only way she knows how to cope is avoidance. If she saw you all the time, it would be something she would become accustomed to seeing. Also, as she grows older, she will learn how to express her questions and thoughts about your handicap. Perhaps next visit her mom should begin to have a discussion with her about it, so that when she arrives it isn't so strange.