It is a real close call for the top 3. I think Winter Soldier is by far the best "Movie", the best crafted piece of cinematic artistry. Like the Dark Knight it is a truly good movie above and beyond its source material and nerd cred. It is one of the few "comic book" movies where even the most dedicated comic book fans did not know what was coming next. Which is a total delight. The fact that they maintained pure suspense throughout it, without compromising the traditional characters, tone or setting, and they turned the entire MCU on its head while telling a tight self contained story was pure cinematic brilliance.
Guardians of the Galaxy is just pure fun, with by far the best most interesting and most fleshed out characters Marvel has yet put on screen. It only suffers a bit from a kind of by the numbers plot and a serviceable but not sexy villain. The movie is all about the main cast and they are wonderful.
Avengers is perhaps the biggest nerdgasm ever put on film, and they nailed it. Plot? honestly who cares? Character development? Why? This is all about putting your favorite heroes on screen together and just letting them go to town. And god damn does it work.