I'd probably rank them, roughly:
Atlanta -- It's just so damn busy, there are some nice ways of managing it, depending on the configuration but even still you just have tons of planes moving around and it's really easy to screw up.
LaGuardia -- It's smaller but I struggle quite a bit with LGA compared to some of the bigger places, the crossing runways and pretty heavy traffic (despite being smaller and only 2 runways) makes for a good challenge. Add having to watch the taxi routes with the terminal layouts and yeah.
Boston -- Another I feel I never get a good hold on, no matter how hard I try =p. The crossing runways and some of the setups can make it tough to keep pushing tin . I have less issues moving traffic around on the ground here, just getting everyone out in a timely matter usually becomes the challenge.
JFK -- With a good schedule, JFK can jump up a bit but generally I find it easy to manage the ground traffic, a bit more difficult getting people out but not as bad as Boston. Pushbacks, for me, is where it usually gets the messiest and trying to not keep arrivals waiting a week to get to their gate =p.
Phoenix -- PHX I've at least been pissed at a couple times, a lot of it is some bugs though. Most part it isn't too bad, the layout is very LAX like, minus a runway, but also with less traffic so it isn't too bad to manage.
San Diego -- It was between SAN and LAS, SAN ends up slightly tougher since you have to remember your exit at commands, and have to be on the ball with getting departures out in a tight window when it's busy. When it isn't busy though, it can be a snore. If you get in a good flow it can be pretty easy, it's mostly just staying on the ball and making sure to make use of exit at.
Las Vegas -- Vegas can be fun, I haven't ran into the traffic jams like I did in 2011 at Vegas, but for the most part it isn't too complicated. watch your crossings and your main taxiway drags and you should be fine.
I didn't include SFO just because I've only played a bit of it, but it'd probably be 2nd right now if I did. Just in my experience with it (a whole hour granted) it is hell to get anything leaving that place during the rush.