This is stated by R. Yaakov Emden in the introduction to "Ets Avot".
Which other sources state that the commentary was not authored by him?
See this short introduction (by R. Mordechai Katzenelnbogen) regarding the commentary of Rashi (page 6 on the site; page 10 of the actual book). He only quotes R. Yaakov Emden (as you did) and R. Tzvi Hirsch Chajes as arguing against the authenticity of the commentary to Avot. But he is certain that Rashi did indeed author a commentary to Avos and attributes their arguments to the inaccuracy of the versions that they had.