I have a recording of Rav Moshe Heineman SHLITA where he was asked this question. He quoted a Gemara in Berachos, which names stars that have a beracha because the residents of those stars came to help the Bnei Yisroel in a milchomo, as a raya that there can be aliens.
Lehavdil BChLCh, Rabbi Dr. Norman Lamm wrote an essay discussing this topic at length. It was published in a book called Challenge. He concludes that there are Rishonim who would accept that the existence of intelligent aliens is possible.