That's really funny that you ask, because I thought the exact same thing when I first read the piece. I don't know for sure why the title is what it is, but I do have a couple of ideas.
First, the title is not "Hally and the boys." It could have been had this play taken place the day before. It's clear that Hally and Sam have a very close relationship. It's clear that Sam loves and cares for Hally deeply. It's also shown that prior to the play, Hally thought of Sam as a kind of surrogate father. "Hally and the Boys" would give the title of the piece a very informal vibe. It would point to the camaraderie that Hally and Sam share. It also would seem to show that Hally and the boys are equals.
The title "Master Harold" comes from the end of the story. That's when Hally angrily demands that Sam call him Master Harold. In Hally's angry mood, he tells Sam that he is nothing more than a servant; therefore, Sam should refer to him as master. Sam responds by telling Hally that if Sam does it once, he will do it forever. That's Sam's warning to Hally. Hally still insists, and the relationship is broken forever.
The other interesting thing about the title is the three periods after "Master Harold." It forces readers to take a big long break and then read "and the boys." What it does is emphasize that "the boys" are an afterthought. They are secondary and less important. "Master Harold and the Boys" could be interpreted to suggest Master Harold and the boys (Sam and Willie) are on equal footing. After finishing the story, a reader clearly sees that Hally does not consider Sam and Willie as his equals. He considers them as tools and pieces of the house, things to be used. That's why the title makes sense. "Master Harold . . . and the Boys" clearly puts an emphasis on Hally's title and the fact that he considers Sam and Willie as mere afterthoughts.
Related to Sam and Willie as mere afterthoughts is the fact that the title doesn't even say "Master Harold . . . and Sam." The title doesn't even give Sam the dignity of being named in the title. Because Hally now thinks of himself as master and Sam as a mere servant, Hally doesn't think it necessary to call Sam by name. A simple "boy" will do, which is incredibly insulting to Sam and Willie.