I don't believe it is Thomas McAllister, however so far we've had more hints towaqrd him than everyone else. In the latest episode, we learnt he was afraid of heights, people may argue that he was up on the roof at the end, but i think RJ would do anything to keep PJ alive, don't you? And just to add he was shitting bricks when the pigeon flew in! and who's afraid of pigeons? That's right,RED JOHN! Just as an extra little bit, probably insignificant, but when on the phone with Jane, he sounded a bit like Red John with a deeper voice! He was also able to read the dead guy quite well! Just my theory:-)