You are welcome. I am going by what you posted, and in the field of molecular / cellular biology, I am a little skeptical that a ranking – whether domestic or international – would have such a great difference in ranking between UCSD and UW’s departments. I know I specifically mentioned the international perception issue, yet I would also suggest at least being aware of what peers in your field may value more highly.
Within the U.S. (and likely some int’l academics who are more attuned to academia in the U.S.), the National Research Council’s rankings for departments usually hold more weight with academics than other types of rankings. They are fairly rigorous assessments, and come out only roughly once a decade, or more (this depends on the sub-field). The only issue with the recent 2010 NRC ranking was that the metrics used made it somewhat more difficult to glean an immediate placement, yet not necessarily less valuable. The overall notion is that major departments do not change so much year to year, and there is a general idea of which departments lead their respective fields.
In your case, both schools are outstanding (if this table below is appropriate for your field) – but you already know this. They are literally placed next to each other in this recent (for NRC) 2007 ranking, and in the top ten both. If this does not cover your field, or provides inaccurate info., I apologize in advance. But this may be quite useful as you prepare for a career in academia. Note: have edited this to add that the entire top ten listed here offers a pretty good snapshot for molecular biology:
http://whichuniversitybest.blogspot.com/2009/06/biochemistry-molecular-biology-ranking.html
Having a faculty advisor whose research aligns closely with yours is indeed a major factor, perhaps most important for your specific career track. I say that without regard to school, campus, etc. Also knowing you will have financial support, facility access, etc. to complete the PhD for most or all of your studies is also a big factor.
At the moment, as UCSD has had some budget issues in the past, now UW may be facing some upcoming budget issues. These issues became public after my first posts to you. It is not clear that they would affect your PhD work at all. At the moment, even if the budget proposals were to go through, so far faculty and facilities should not be impacted (more like classified staff, etc.).
You may consider contacting the potential advisors at one or both institutions to ask questions if possible, if you have not done so already. If there are any concerns such as you’ve mentioned, or about maintining support toward the PhD, perhaps they could assist you more.
Hope this helps. I don’t think you will make a bad choice between these two. Congratulations-