It's in contention between JLU, EMH, and YJ.
JLU probably has the lead - it really has nothing wrong with it. Strong cast, great performances, balance between serialized storytelling and villain-of-the-week stuff. Animation is rarely amazing, but doesn't ever let you down, either. And while the original JL is a bit iffy in spots, as a whole it's super consistent.
EMH pretty much takes the template of the DCAU and applies it to Marvel - like, in retrospect, it's an incredibly impressive show, considering how often they've dropped the ball. It struck that same storytelling balance, juggled a cast just as huge, and even more than the DCAU, did a phenomenal job adapting the entire Avengers history into a TV show. Like, the transition of Nick Fury from a 616 type design to the Ultimate one was inspired. I really need to give this one a rewatch. Of course, it was cut pretty short, and the back half of the second season wasn't as strong.
YJ is, of course, the absolute king when it comes to intricately plotted storylines and character dynamics. It's remarkably consistent, and creates a world that's just fascinating to read about - like, even just going through the wiki is a ton of fun. The animation has definitely taken a hit since the revival, but that doesn't necessarily bother me much... even if it can get distracting.
I don't think any of the others really compare. TT and X-Men: Evolution are both solid, but neither reach the heights of those three.