It all depends on what you want to shoot. Each park has an advantage and a huge disadvantage... as follows:
Epcot : You can slowly make your way around the world showcase and take pics pretty long after the park closes, but don't count on futureworld. They close that off early and unless you are there already, you have no shot. Morocco is one of my favorite night time spots to shoot in the entire resort, and I mean.... everybody needs the obligatory spaceship earth long exposure shot
The park is also not open as late as MK so you can still stay after close and get some good sleep in.
MK: Park is a lot more crowded and has far more people lingering around long after close, even at a 1am EMH. You will still get some great shots, but you will need to be super patient. People will walk in your shot, and people will drive by with ECVs with bright lights on them, ruining a long exposure. Comes with the territory.
Another downside to MK is their closing "Sweep" is unpredictable. Some nights I'm able to stay 2+ hours after close, others... they ask me to leave before even an hour after. Hit or miss, really. You also risk not getting to do all the lands after close, as they section parts off as they empty out. Tomorrowland is the most challenging of the bunch to shoot, followed shortly by New fantasyland (for exact opposite reasons, oddly enough).
The most important thing to remember is to be nice and listen to any CM that approaches you with a request to re-locate. They are usually nice and let you hang out a bit longer if you are kind and social (this goes for security guards as well).