I think there are many examples of Tom coming of age. When he gets the boys to whitewash the fence, using reverse psychology, because he doesn't want to do it. How many present day kids could do that? He falls in love with Becky and imagines and stages his own death, quite a thinker. The later engagement to Becky and Tom's admission of a prior relationship shows honesty.
After the murder of Dr. Robinson, the boys swear to remain silent. The later rafting away exemplifies guts and fortitude. When he exonerates Muff at the trial is another excellent example of his honesty and wanting to do the right thing. Later when he hides in the caves with Becky, even though some would say this depicts his childish nature by hiding, I think it is another example of him having courage and certainly coming of age.