This is a great question. Of course, you are going to get a wide range of responses. We are presented with a whole series of characters who are suffering in one way or another. One approach is to think that in a sense, it is Joe Keller who is responsible for all of their suffering through his act of deception and his lies. Therefore, the inner guilt of Joe could be said to prove that he suffers more than anyone else.
However, for me, I feel that Kate Keller's suffering is actually worse than Joe Keller's suffering. Joe in the play seems to be doing his best to put the past behind him and to get on with life. However, Kate Keller, because of her husband's lie, is shown as being unable to move on, in particular she is unable to accept the reality of the death of Larry:
I want you to act like he's coming back. Both of you... Because if he's not coming back, then I'll kill myself!
For her, to admit that Larry is actually dead is synonymous with admitting the guilt of her husband in the death of the pilots because of the faulty parts that Joe Keller's factory produced. This is why she must cling so ferociously to the past, thereby preventing others from moving on as well.
Therefore, in my opinion it is Kate Keller that suffers more in this play.