I wouldn't rule out Stanford. I think very few people live in San Francisco and go to Stanford, and there is a similar cost of living closer to Stanford as near MIT. Stanford also has much nicer weather year-round and the OR/IE track has good job placement. The difference between weather near Cornell and MIT is negligible compared to how nice Stanford is all year.
That said, I think you should look more at the faculty at each university and try to find potential supervisors, maybe contact them and see what your options are. If you wind up doing something you don't enjoy or aren't enthusiastic about, that will be a bigger problem.