Most likely Shamrock, though possibly Garling.
I could also see it being Sommers or another Knight.
Odds seem to be pointing toward Shamrock for now, imo.
I don’t think Oda showed Garling disposing of his sons’ mother to imply he would do the same thing with Ginny.
I think we will learn Shamrock is the father, and I think we will also learn the circumstances of Bonney’s birth are directly tied to not only Shanks’ tenure in the Holy Land, but also Uta and her mother - who I now suspect may have been desired by both Figardland brothers, but chose the younger twin, to the anger of the elder twin.