For my application HBS, I had an old professor of mine write a recommendation. This was a good move for me, but only because:
a) He knows me well and has had a ton of interaction, so he could speak about me as a leader, academic and professional.
b) I supplied him with a well-crafted game plan so that he could get a better idea of my career goals and professional activities and reflect those in his recommendations.
If you have a) and can produce the information in b) then I think having a professor for MIT and HBS can help. If you can't get a & b, the then option 1 might be best.