Our version of the Ibn Ezra actually does not have him quoting anyone, but rather saying that idea in the name of many.
The Rav Kook edition of the Ibn Ezra has second section with a variant text which does find him quoting this in the name of The Nagid. The footnote there says this is indeed a reference to Rabi Shmuel Hanagid, and sends us to the introduction section of the seffer where all the people quoted by the Ibn Ezra are mentioned.
There is a list there of all eight times Ibn Ezra quotes Rabi Shmuel Hanagid.
Bereishis 19,18. 33,10. 49,18. 49,23.
Shemos 6,3. 32,31.
Bereishis variant text 17,1.