They are not related, and I can get pretty close to proving it.
In The Tommyknockers, there is a reference to the movie version of The Shining. In the novel It, a younger version of Dick Hallorann makes a cameo appearance in one scene. Therefore, The Tommyknockers takes place on a level of the Tower where Stephen King exists, and wrote both The Shining and It.
Hence, Pennwyise does not actually exist in The Tommyknockers. (That said, let me play devil's advocate to myself and note that there is a section in which one character, while in Derry, imagines that he hears laughter coming from a drain. That's clearly a Pennywise reference, so it leaves the door open. My explanation for that is that this character has read the novel It, and is letting his imagination creep himself out. Kind of a stretch, but not a big one, really.)