The TNG episodes seem to indicate the Klingon Empire is stronger, which doesn't seem to make much sense, given that the Federation's culture promotes technological advancement, and the unity of the different species within the Federation would give Starfleet resources that the Klingons, who subjugate species, wouldn't have.
DS9 seems to indicate that Starfleet would win. First of all, while the Klingons were attacking DS9, Worf says "The Empire is not strong enough to defeat both the Cardassians and the Federation." In another episode later on, Worf's brother says he opposed the war with the Federation because he believes that the Federation is powerful, and that the Klingon Empire may not necessarily win a war with the Federation.
All in all, DS9 gives us the indication that the Federation is more powerful, and since DS9 is the series that takes place farther in the future, I'd have to say that the Federation would win.