<p>I second what boneh3ad said. </p>
<p>The strength of the specific PhD program/department is almost always more important than the overall reputation of the school. I would assume that schools like Caltech or MIT most likely have strong PhD programs in most or all areas. However, you also will find stellar graduate programs in schools that USNWR has ranked as 3rd tier. There are also weak graduate programs in otherwise highly ranked schools, so it is not always safe to assume that the overall reputation of the school directly translates to uniform quality among all of its departments or programs.</p>