He doesn't see it at first, he just thinks they're good friends, but once Jane lives with him briefly he comes to realise that his sister has feelings for the doctor, and the doctor has feelings for his sister. He wants to shout it at the two of them, wants to rub it in Jane's face that he's noticed something before she has. He wants to shout from the rooftop that he's seen something that the great Detective Jane Rizzoli has missed, and something so obvious too.
But he doesn't, he just sits back and watches the two of them, a smug feeling always in his heart when the two of them are together.
It only gets worse once his Ma moves into Maura's guest house, and Jane starts spending more time there than she does anywhere else except work. It's hard to watch sometimes, he just wants to grab them and lock them in a closet until they work it out.
But he can't do that, he likes being in one piece and if he even tried to do anything like that Jane would rip him to pieces. So he just waits, smug in the knowledge that he knew before either of them did.