The only issur relating to negiah with a penuyah tohorah is the potential hirhurim which would be a violation of Lo Sosuru. Where there is no Chashash Hirhur, which I hope would be the case with respect to a 3 year-old niece, there is no issur.
The only possible issue is the Rambam’s declaration that hugging and kissing an Aunt is disgusting. Whether that would apply to young child is unclear, it would depend on the reason the Rambam held it was megunah.