Can the mom of my 16-year-old girlfriend file harassment or stalking against me for talking to her if she wants to to talk to?

Technically she can as the parent of the minor child, but she would have to show that your conduct amounts to stalking or harassment. If not, then I doubt if any charges will be filed. If so, then you must understand that even though the daughter wants to communicate with you, if your actions amount to stalking or harassment, then the prosecutor can take into account both the daughter's and her mother's wishes to prosecute because she is still a minor.