The issue of surrogacy and determining whether parenthood depends on genetics or on birth is very complicated in halacha and difficult to prove. See here for an article by Rav Zalman Nechemia Goldberg Shlit"a where he proves from various sources that the mother who gave birth to a child is considered the mother in halacha, not the mother who donated the genetic material. This is not the forum to weigh in on such a major topic but one of the cases in our mishna opens it up for discussion.
Regarding fatherhood, it would seem that it is determined by the one who contributed the semen, since that is the only active role the father takes in producing the child. However, we find that if a man would have relations with a non-jew, the child born would not be halachically related to the father. Rashi writes that if a woman converts while pregnant, the child wouldn't inherit from the biological father since conception happened with a mother who was a goy, the Torah no longer connects the semen to the father - דזרע מצרי רחמנא אפרקריה דכתיב וזרמת סוסים זרמתם. Tosafos agrees, but comments that if the mother converts while pregnant, the child anyway isn't related to the father because the child is considered a convert and גר שנתגייר כקטן שנולד דמי breaks his relationship with his biological family. Therefore, it would seem that in a situation where the bio mother and the surrogate mother are both jewish, we would consider the father to be the father. But, if either one is not Jewish, whether the father is considered the father would seem to depend on who is the mother. If the bio mother is considered the mother, perhaps we would consider the bio father the father even though his semen eventually was placed in the uterus of a non-jewish woman. But, if we consider the surrogate mother to be the mother, the biological fathers connection would likely be broken as well.
It seems that the answer to who is the mother may also lie in this case. When a woman converts while pregnant, we consider the child born after conversion to be a bechor regarding pidyon ha'ben - he is the פטר רחם. It would seem that before we entertain the ability of the child to be considered the פטר רחם of this woman, we must first consider him the child of this woman. The gemara says in Yevamos 78a that when a woman converts while pregnant, the conversion works for the child also and he is considered a convert (the womb isn't a chatzitza for the tevilla). Since we would apply כקטן שנולד דמי at the time of conversion, we would not consider the woman pregnant with her own child (even if conception would normally determine motherhood), yet when the child is born we consider him to be a פטר רחם. It would seem that birth determines the relationship between the mother and child because otherwise we shouldn't consider this child to be the פטר רחם. One can disagree with this logic by underlying the assumption. Perhaps motherhood is not a prerequisite for this child to be a פטר רחם. Therefore, even though we wouldn't consider him to be the child of this mother, he would still have kedushas bechor for pidyon ha'ben.
R. Zalman Nechemia cites an excellent proof that it is dependent on birth from the gemara in Yevamos 97b that says when a woman converts while pregnant with twins, the two brothers are considered brothers for the prohibition of אשת אח (if one would have relations with the others wife after he dies). Even though conception would not consider them brothers because they went through a conversion in the process, the halacha still considers them to be brothers because they are born from the same womb. Just as the relationship between the two brothers is determined at birth, the relationship to the mother should also be determined at birth. According to this approach it is not gestation or incubation of the surrogate mother that would determine her to be the mother in halacha, because the gemara indicates that the same halacha would be true if the mother converted well into her ninth month, a day prior to the birth of the child. Rather, it is the actual birth that would determine the familial relationships.
Rav Zalman Nechemia points out that the gemara in Chulin 70a would seem to imply the exact opposite. The gemara discusses a case where an animal gives birth to a bechor directly into the uterus of another, the second animal then gives birth to this bechor and the gemara wants to know whether a child that doesn't belong to it can exempt it from bechor (in the future). The implication of the gemara is that the child doesn't belong to the second mother, even though it also gave birth to it. However, Rav Zalman Nechemia rejects this proof. He points out that since the first animal also gave birth to it, the child already has a mother, therefore the second mother isn't considered a mother. But if the surrogate mother is the first to give birth to the child (as a viable human being or animal), the surrogate mother would be considered the mother.
According to Rav Zalman Nechemia Goldberg the proof from Yevamos 97b is sufficient evidence that the family relationship is established at birth, therefore the surrogate mother is considered the mother. It would therefore follow that if he surrogate mother were a non-jew, even if the genetic mother was jewish, the child would not be jewish.
However, my uncle, Rav Shabtai Rappaport has a very unique (and complex) approach to this issue that I found in an article online - see here. He considers the gemara in Yevamos 97 evidence for determining the family relationships in regard to עריות but not for the purpose of determining status as a Jew. He suggests that the fact that the gemara in Yevamos 78 considers the child of a pregnant convert to be going through his own conversion, implies that the child's religious affiliation is determined at conception by the genetic mother. Since the genetic mother is a non-jew at the time of conception, the child would not be a Jew unless we consider him to have undergone his own conversion. Even if the mother converts while pregnant and the child is born to a Jewish mother, this would not transform him into a Jew since his genetic material wasn't Jewish at the moment of conception. In the case of surrogacy it would then follow that the surrogate mother is considered the mother, but the genetic mother determines whether the child is a Jew. When the surrogate mother is a non-jew and the genetic mother is a Jew, the child will be Jewish but his "mother" will be the non-jewish woman.
The approach of Rav Shabbtai Rappaport is novel, but it is odd to separate between the question of who is the mother and the one who passes on the Jewish "gene". To me it seems that the proof from the pregnant mother converting doesn't force us to say that Jewishness is passed on by the genetic mother. Perhaps if the mother were able to convert without also converting the fetus she is carrying, the child would still become Jewish upon birth from a Jewish mother. But, since the conversion of the mother automatically works on the child that she is carrying, the child is considered Jewish due to conversion rather than a result of being born to a Jewish mother.
According to Rav Zalman Nechemia Goldberg the proof from Yevamos 97b is sufficient evidence that the family relationship is established at birth, therefore the surrogate mother is considered the mother. It would therefore follow that if he surrogate mother were a non-jew, even if the genetic mother was jewish, the child would not be jewish.
However, my uncle, Rav Shabtai Rappaport has a very unique (and complex) approach to this issue that I found in an article online - see here. He considers the gemara in Yevamos 97 evidence for determining the family relationships in regard to עריות but not for the purpose of determining status as a Jew. He suggests that the fact that the gemara in Yevamos 78 considers the child of a pregnant convert to be going through his own conversion, implies that the child's religious affiliation is determined at conception by the genetic mother. Since the genetic mother is a non-jew at the time of conception, the child would not be a Jew unless we consider him to have undergone his own conversion. Even if the mother converts while pregnant and the child is born to a Jewish mother, this would not transform him into a Jew since his genetic material wasn't Jewish at the moment of conception. In the case of surrogacy it would then follow that the surrogate mother is considered the mother, but the genetic mother determines whether the child is a Jew. When the surrogate mother is a non-jew and the genetic mother is a Jew, the child will be Jewish but his "mother" will be the non-jewish woman.
The approach of Rav Shabbtai Rappaport is novel, but it is odd to separate between the question of who is the mother and the one who passes on the Jewish "gene". To me it seems that the proof from the pregnant mother converting doesn't force us to say that Jewishness is passed on by the genetic mother. Perhaps if the mother were able to convert without also converting the fetus she is carrying, the child would still become Jewish upon birth from a Jewish mother. But, since the conversion of the mother automatically works on the child that she is carrying, the child is considered Jewish due to conversion rather than a result of being born to a Jewish mother.