Joe Harper is Tom's best friend and partner in crime. Their friendship is really quite simple. The boys enjoys doing the same things: playing hooky, pretending to be Robin Hood, and just generally having fun. Joe's role diminishes as the novel goes on, however, and by the time Tom gets to treasure-hunting Joe has pretty much fallen off the radar. The question is: why?
For one thing, Joe has no part in Tom and Huck's trip to the graveyard; he does not see Injun Joe murder Dr. Robinson. It's this traumatic event that brings Tom and Huck together and sets the rest of the plot in motion. Joe simply isn't there for it. The later parts of The Adventures of Tom Sawyer have so much to do with Injun Joe that it just doesn't make much sense for Twain to add Joe Harper to the mix. Not to mention, trying to talk about two Joes, one a scary man and the other an innocent boy, at once gets confusing.
Putting these technical questions aside, here's another consideration: Joe doesn't really have as much freedom as Tom and Huck. Huck, of course, has no obligations to anyone and Tom, well, he's Tom…he does what he wants. Joe, however, has the most traditional family structure; he has a mother and a sister and, one guesses, a father. He also seems to be a bit shyer than Tom and Huck. When discussing possible career alternatives, Joe's first choice is being a hermit. Kind of a weird choice for a kid, no? Well, that's the way it is.