It's probably the Galaxy-class, though I don't believe there's canon proof of this; all we know for sure is that it's one of the largest Federation ships. Note that if you extend the realm of possible answers to include non-canon works (books, games, etc.), enormous vessels bigger than the Galaxy-class are surely a dime a dozen.
Further to the above, it can also depend on a few details and their definitions. The Sovereign-Class (i.e. Enterprise E) was longer than the Galaxy class, though it had fewer decks. There may have been ships whose dimensions were smaller than a Galaxy class vessel but had a larger internal volume. Also, it's fairly accepted that even into Voyager's timeline the Galaxy class was the largest Starfleet vessel - however this does not make it the largest Federation vessel (freighters, civilian transports, medical ships etc might have trumped the Galaxy class). As the series' progressed, there did seem to be a tendency in Starfleet towards building smaller, faster and more manoeuvrable vessels, possibly to exploit the few advantages Starfleet vessels had over Borg ships?
The Galaxy class was just beaten by the Galaxy Dreadnought due to it's extra Nacelle in any case. If you would like to believe Star Trek Online, it has made an "Enterprise-F". The -F is an Oddysey class and is supposedly bigger than the Galaxy Dreadnought but I haven't tested that ingame.