There is no mention of the miracle of the פך שמן:
In Sefer Hamaccabim 
In Josephus 
In the Raavad's Sefer HaKabbalah
In the Al Hanissim Tefillah
In הנרות הללו
In the Megillat Taanis 
In the Pssikta D' Rav Kahana
The פך שמן makes its first appearance in the Baraisa added to Megillas Taanis and in the Megillas Antiochus.
In any event it would seem clear that the פך שמן only became an important feature of Chanukka at a much later date. 
Two possible suggestions for this new focus for Chanukka are:
1- The Chasam Sofer (and somewhat similarly Kaufmann Kohler in his JE article), suggests that the reason why there is little mention of Chanukka in the Mishna is because Rebbi who belonged to the house of the Nossi and was a descendant from Dovid Hamelech (אנן מן הזכרים) resented the usurpation of the Malchus by the חשמונאים. To put it more plainly perhaps the Pharisees unhappy with the Saducee influenced- כחי ועוצם ידי- חשמונאי rule decided to downplay their military achievements and focus on a more spiritual aspect of Chanukka.
2- R' Reuvain Margolies (See my section in Wikipedia Mishnah on this) suggests that as the Mishnah was redacted after the Bar Kochba revolt, Rabbi could not have included discussion of Hanukkah which commemorates the Jewish revolt against the Syrian-Greeks (the Romans would not have tolerated such an overt display of nationalism). If so possibly at that time the נס of the פך שמן was given as the main reason for the celebration so as to avoid giving the Romans a reason to suspect revolt (similar to the reason that Shofar blowing was pushed off to Mussaf).
 See the article מאי חנוכה in the periodical אור מזרח wherein the view of Yaakov Reifmann is cited that the non-jew who translated it from the Hebrew deliberately left it out because it seemed to him incredible. See בינו שנות דור ודור who pints out that Maccabees II which generally focuses on miracles is in its original language.
 "From that time onward unto this day we celebrate the festival, calling it 'Lights'" (Φῶτα, Ant. 12:325). He explains that the festival acquired this name because the right to serve God came to the people unexpectedly, like a sudden light (ibid.).
 Actually our version of Megillat Taanit does mention the נס but in the critical addition it is noted that this is a later addition (scholium). The Megillas Taanis (and the Pesikta) appears to say that the נס was that they found pure שפודין to make into the Menorah.
The fact that the נס isn't mentioned earlier should not cause significant doubts over its veracity for according to the account of Maccabees II it would appear that ניסים in the ביהמ"ק were commonplace (or at least considered so by the populace) and would not have been the centerpiece of the Festival.
[Edit: I missed this article at JPost . His main arguments -
"We see that it assumes that the high priest was a person of impeccable integrity. Second Maccabees tells us quite clearly that this man was Menelaus, a rogue of the first water.
They did not know that the High Priest at the time the Hasmoneans forced their way into the Temple was Menelaus, who was guilty of bribery, stealing the Temple gold, and murdering the former high priest Honia. If they had known that, would they have seen the seal of the high priest as a guarantee of purity, would they have seen a miracle in a cruse of oil sealed by such a high priest."
His proof would depend on the nature of this seal. There may have been ways of identifying which seal was placed by which Kohen Gadol. If so they may have been able to identify that the seal belonged to an earlier righteous Kohen Gadol. Alternatively - Who said Menelaus was involved in the production of oil at all? He seems to have had other concerns on his mind. I doubt he would have been much concerned about procuring and sealing pure oil. All in all his thesis still has a long way to go.]