After one season with Colorado, Zeile became a free agent again and signed with the Yankees in 2003. He was released mid-August and was signed by Montreal three days later. Having decided 2004 would be his last season, Zeile returned to the New York Mets. He also voiced displeasure with the Yankees, saying that he has "no desire to play again for that organization", and that "I think some of the things that happen over there are different than any other organization in baseball. I have a pretty good track record to judge that."