Ackman at Delivering Alpha: Buy Fannie and Freddie

Bill Ackman reiterated his support for nationalized mortgage lenders Fannie Mae and Freddie Mac, during an appearance Wednesday at the Delivering Alpha conference.

Ackman has talked up the two lenders before, but said "no one's really noticed." Fannie is up about 11 percent in 2015 and Freddie is up nearly 4 percent.

"It offers the most upside, probably the most downside of anything we own," the head of Pershing Square said. He believes the downside scenario is unlikely.

The federal government bailed out the two government-sponsored enterprises during the financial crisis.

"This cannot become a precedent where the U.S. government can come in and unilaterally take 100 percent of the profits of a private corporation forever," he said.

Read MoreDelivering Alpha: Activists' hit list

Fellow activist investor and head of Trian Fund Management Nelson Peltz took the stage with Ackman but was more circumspect about his best investing idea.

Bill Ackman at Delivering Alpha 2015 in New York on July 15, 2015.
David A. Grogan | CNBC
Bill Ackman at Delivering Alpha 2015 in New York on July 15, 2015.

He said only that he has two new ideas, one of which is an industrial company and the other which "we have not categorized yet." Earlier this year, Peltz disclosed a stake in Pentair, a pump and valve maker.

However, he did take a minute to defend the nature of activist investors, who have been at the center of an animated public debate. Critics say activists are short-term raiders looking to maximize profit without regarding to fundamental growth of their targets, a charge Peltz rejected.

"They talk about the fact that we're short-term, they talk about how we like to lever up, they talk about all this stuff," he said. "What really troubles me is all the mudslinging that goes on with activists."

He pointed to Wendy's and Heinz as examples of companies in which he took a stake and has shown long-term commitment.

Peltz, who lost a high-profile battle at DuPont earlier this year, also said McDonald's needs a major cultural change though he said he would contemplate taking a stake if he didn't own Wendy's.

Peltz also was critical of Alexander "Sandy" Cutler, the chairman and CEO at Eaton. He said Cutler should not hold both roles. There has been speculation that Peltz is targeting the company for an activist move.