First off, congrats on your acceptances!
I'm still looking at programs in BioE, so I'm sure there are people who might be able to give you a better idea of what it's like to be at each program. Actually, I wasn't even aware that Yale offers a master's in Bioengineering (could you share some information about that?). However, I'm a strong proponent of the joint program at Cal/UCSF. You get access to two renowned institutions (one in engineering, one in medicine) at once, which should give you all the resources and opportunities you could want to further your academics or career. The master's program at Berkeley-UCSF is definitely focused on those who wish to enter industry because the core curriculum consists of more industrially relevant topics, like biotechnology entrepreneurship and strategic management, as opposed to being mostly pure science or engineering courses (but of course, you have the option to fill your elective slots with more industrial-type or more pure science to customize your education just the way you like--which is great).
No doubt that Yale is a great program also, but if your only plus from Yale is it's name, I don't think it's worth it at all. Honestly, I think you might be able to impress more people who are not knowledgeable about life sciences with the Yale name, but for experienced people, as in industry, the Berkeley/UCSF name is just as good if not better.
