juluca

I think it depends on what you think you might want to do after your PhD. If you want to stay in academia then, at a topical level, Baylor has a stronger reputation for research. If not, then its important to look at what services the schools provide you with respect to career development. Apart from that, if the research fit is good for you at both places, think about which place you would be happier living in, and where you want to build your network.

Well, I, for one, totally think you should come to UM PIBS so we can be classmates. Also because you can tell people where you live by using your hand as a map, since you'll be living in The Mitten! Put those points in your pro-con list 
As far as reputation goes, they're all fantastic schools, you really can't go wrong. I was rejected from Northwestern DGP and UW Neuro, but Michigan was at the top of my list anyways so I'm pretty content with how that shook out. I also echo the other commenter's position that it looks better to not stick around at your undergrad institution for grad school. However, if you have strong reasons for sticking in the Seattle area, that's also an important consideration.
If you were at the PIBS interview weekend, you probably saw their post-PhD job placement stats at Saturday breakfast, and personally, I was really impressed with them. My current PI is a UM PIBS alum and he's going off to a TT position in the fall, and he only graduated in 2013. Obviously n=1, but he speaks very highly of UM's job network and felt supported there as a student. I also think, though, that you won't have significantly more issues with job placement at one of these schools compared to the others, as they're all high-caliber institutions. I don't know about UW or Northwestern, but UM seems to have more students placed into academia post-grad, but a healthy % also go into industry. I imagine UW might have connections in the PNW biotech industry, however, and from my understanding, Seattle is a pretty big biotech hub  - so there's that to consider. 
As far as breadth goes, I also think you're likely to have plenty of faculty options at any of these schools. UM PIBS has over 500 faculty, and it seems like a LOT are currently looking for students. I imagine, however, that Northwestern and UW have comparable faculty lists. In terms of student community, that's something you'll have to evaluate for yourself I'd imagine. I loved UM's neuro department because the students and faculty were very close knit and friendly - it felt like a slightly bigger neuroscience community than the one I have here at my undergrad, and I really liked that. Is there a student host you interacted with on your interview weekends who you could reach out to and discuss some of your questions/concerns with? I  communicated with several current students at the two programs I chose between, and it was really helpful in my decision-making process. 
I think something that hasn't been discussed yet is location - where do you see yourself spending the next ~5-6 years? Downtown Chicago is going to be a very different living environment than suburban metro-Detroit. Ann Arbor is a large college town, sure, but it's very much a college town, and not a sprawling city. I'm a born & raised Michigander who's moving back to the state for grad school, currently living in Ohio. Personally, I didn't really want to live in a big city, and I really enjoy the size and feel of Ann Arbor. However, it is bitterly cold here some parts of the year, and you should take things like this into account when deciding if you could be happy living in either of these places. If you have any more specific questions about southeastern Michigan/Ann Arbor/metro Detroit, feel free to PM me - I grew up in the area and know a lot of students currently at UM, including 2 PIBS students. 
Whew, that ended up being long. Definitely not trying to push UM, it just happens to be the school I have the most info on! I would say that you should think on where you think you'll be happiest - Chicago, Ann Arbor, and Seattle are very different cities, and you're going to be spending the next 5+ years at this program. I'm a firm believer that the more balanced, happy, and supported you feel in your program and by your mentor/lab mates/colleagues, the better work you'll produce, and the more productive your grad school career will be. Congrats on having these awesome options to choose from! Feel free to reach out if you'd like to chat about UM, living in the midwest, or anything else I could help with 

If you're interested in going into industry after academia, then what you'll be looking for will be different than other graduate students. You'll have to find PI's that are open and supportive of the idea knowing that you'll be going into industry after graduate school. Some PI's I've met with through my interviews were clearly more open about it than others. Some even have direct connections and will help you get a job in big pharmaceuticals after you graduate while others may be more biased about industry and try to keep you in academia. I feel like all three schools have excellent research strengths in the biomedical sciences - all with great reputations. I don't know about other states but in Texas, UMich and Northwestern are highly regarded, more so than University of Washington. That's just 'laymans' prestige. But of course, in academia, all three medical schools have excellent research programs.
I'm in the same situation as you and trying to decide between NYU Sackler or Baylor College of Medicine for virology/immunology. so if any of you have insight into those schools it would be greatly appreciated!
Some schools will publish where their students go after they graduate. At NYU, 70% go into industry while 30% continue onto postdoc. At Baylor, 70% go into postdoc's while 30% go into industry. So the culture at the two places are already different in what they will be best preparing you for.
Also, in my opinion, it looks better to go to graduate school at a different institution than where you did your undergrad. I think the same would also considered to be true for post-doc. You generally want a greater breadth of educational experiences from different schools than staying at the same place for all the stages of your education.