Skadi seems to marry Njord after Freyja and Freyr are born. The only other figure I can find is Nerthus, though information on her seems scarce.
While Njord was with the Vanaland people he had taken his own sister in marriage, for that was allowed by their law; and their children were Frey and Freya. But among the Asaland people it was forbidden to intermarry with such near relations.
The same thing is implied in the Lokasenna, when Loki claims
"Give heed now, Njorth, | nor boast too high,
No longer I hold it hid;
With thy sister hadst thou | so fair a son,
Thus hadst thou no worse a hope."
However, the Gylfaginning implies that the mother was indeed Skadi:
Njördr has to wife the woman called Skadi, daughter of Thjazi the giant.
. . .
"Njördr in Nóatún begot afterward two children: the son was called Freyr, and the daughter Freyja; they were fair of face and mighty.
The claim that the mother is Nerthus seems to be mainly based on etymology, and not on any specific writings.
There is another candidate for Njord's sister: Njorun. Her claim isn't a lot better than Nerthus', based mainly on linguistic similiarity. Njorun turns up in a list of goddesses, and in kennings. (Dream-Njorun, for night, appears in Alvissmal.) You can read more about the case for Njorun, but the identity of Njord's sister/wife is clearly one of those mysteries that will never be resolved.