An interesting question.
Here are some similarities. Both are outcasts in their town. Both are the subject of much whispering and gossip. Both are objects of fascination for Scout and the rest of the town. Both serve as moral lessons for Scout; both are the targets for irrational fear. Both are arrested at some point in their lives, but both are essentially good.
The differences are marked. The most obvious is that Boo is white and Tom is black. As a result, Boo, while he is kept in the house, is protected from a lot of social fall out. Tom, by contrast, is punished far beyond any actual crime he's done, by society. He is eventually killed. Both are "mockingbirds" in the book's symbolism, but Boo is protected and not killed. (Tom, of course, is physically handicapped—one arm is crippled.)