At a time when many university endowments have been reporting lackluster or even negative returns, Yale has turned in a winning year. The university said on Friday that its endowment earned 3.4 percent for the fiscal year ended June 30, putting its value at $25.4 billion. The Yale endowment, under the leadership of David Swensen, has long been a top performer. Its latest showing is particularly striking since the average among endowments that have reported so far is a loss of 2.7 percent, according to Cambridge Associates, which manages over $9 billion for foundations and endowments.