I'm applying for chemistry program, but I think that the discipline is not so important in that case. I would definitely opt for the school with a better advisor. This is the person which (apart from you) has the biggest impact on your success in graduate school. I've been doing research for some time and I know what I'm saying. Bad advisor can take away all the joy of research. So I would chose the school with less reputation:)
So guys, do you have any info what are the average sizes of the new graduate classes in chemistry? How many people do they take at each program? What is the difference between large and small program?
Regarding MIT, I contacted Lynn Marie Guthrie and got information that the majority of applicants will receive a decision by the last week of February.