It's hard to attribute any specific tone to the play since there is no narrator, but there are a few things to note. Much of the humor of the play derives from irony, when the characters have attitudes that seem out of place with their situations. For example, there's that moment when Hamm and Clov discuss so calmly how Hamm will know if Clov has abandoned him or if Clov is simply dead in the kitchen. Their reasoned arguments just don't match the seriousness of what they are discussing.
That said, the characters are always aware of the absurdity of their situations. We think that this might make it a more sympathetic ironic tone. An unsympathetic ironic tone would be one in which the author and the audience are aware of the irony but the characters are not; the characters aren't as bright as everyone watching them. In this play, though, they are pretty on top of things.