I assume that you are thinking about various movements in the '60s as separate countercultures. In other words, I assume that you are saying that the Women's Lib people were one counterculture, the Hippies another, and so on. If so, I would argue that the Women's Lib/Feminist counterculture was the most important and influential.
I would argue this because I believe that the women's movement did the most to change US society. I think that many of their goals were achieved to a greater degree than those of other countercultures. I also think that the movement had impacts that would have been difficult to foresee at the time.
Just to give one example, I am male but have had only part-time jobs since my first child was born. At that point, I quite my full-time teaching job to stay home with the child (later, the children) while my wife worked. I know quite a few other men who do this. That would have been unheard of in my parents' generation (they were adults before the counterculture days).
As another example, my mother was not allowed to wear pants on the campus of her public university in the early 1960s. That sort of paternalistic attitude towards women has changed drastically.
Finally, the feminist counterculture has had other impacts that might not have been anticipated. For example, the American family has changed greatly since the '60s. Divorce and remarriage are common now. This is something that has come about as women have gotten more rights, more education, and more of the mindset that they should assert themselves in relationships and demand fulfillment.
So, I would argue that the feminist counterculture was the most influential of the era.