The best of the big guns has got to be Hulk, Thor and Juggernaut bar none. But who do you like for your team?
The Hulk is by far the best character at fighting bosses. His charge/tackle and gamma pound can do mega damage to bosses and overwhelm them. I don't know of another move in this game that does more on a single attack than the Hulk's charge! Just huge, huge damage!!
But Thor and Juggernaut have him beat when it comes to playing the game and taking on the swarms of enemies that attack you. Thor is better than Juggernaut when it comes to versatility, range and immunity to electrical attacks. Plus Thor is so incredible with his more consistent damaging attacks and fusions. Team Thor with Spidey, Iron Fist or Daredevil and you'll get the best and most damaging fusion in the game period. Juggernaut just has his insane charge that causes tremendous damage to swarms but all his other attacks are sub-par. But he is able to resist and take more overall damage than Thor and he seems to be equal to the Hulk this department as well.
Here is how I list them:
Overall single move damage: Hulk Charge/Tackle
Overall damage with total moves: Thor
Best crowd control: Thor, Juggernaut Lightning Rod, Juggernaut charge (tie)
Best Fusions: Thor
Best against Bosses: Hulk
Best resisting damage: Hulk, Juggernaut (tie)
Best as back up character: Hulk, Juggernaut (tie)
As you can see, either way Hulk, Juggernaut or Thor is a must on ANY team.