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I had to make this same choice (actually my final 2 were Boston and Minneapolis), but Seattle was only eliminated late in the race.
Unless you make really good money, I would think it'd be very hard to afford a home in a decent area in either Boston or Seattle. Especially Boston, where structures comprised of termites holding hands sell for $400,000. I had a 300 sq. foot basement apartment in Boston and paid $1,100 a month. Outside of Boston, you're still in New England, and you'll be charged as such. I believe prices begin to fall considerably once you get a bit outside of Seattle.
Is being reasonably close to family a consideration? This was the deal breaker for me with Seattle. My family were all in Georgia at the time, and Seattle was a world away, plus it was a 3 hour time difference. Boston wasn't exactly next door, but it was the same time zone, and I could get back to GA much quicker by plane or car if I had to. The time zone thing also bothered me from other perspectives, such as football games being on at 10 in the morning. That was too weird.
Had natural beauty been the only factor, I would have been in Seattle instantly. To this date it is the most beautiful metro area I have ever seen. The combination of snow capped mountains, vast waters, and evergreen forests is nothing short of fabulous. I still think of the first time I saw Mt. Rainier while getting on the freeway out of the Sea-Tac airport. Unbelievable! Boston is a lot hillier than one who had never been there would imagine, but most of it has been built upon. Still, Boston's architectual splendor is hard to beat. So many wonderful, historic places and beautiful, old buildings.
If you plan on being a city dweller, Boston is better. I got rid of my car when I moved there and used public transportation for everything. Very walkable town, too. I lived in Back Bay and could easily walk to my job in the South End, to Fenway Park, the Commons, downtown and the harbor, across the bridges to Cambridge.....you name it. I don't think you could live that way in Seattle. They have a lot of freeways and a lot of ferry's you need to get where you're going.
Weather-wise it's a toss up to me. I like snow in the winter, and Boston definitely gets more, but Seattle averages 15 inches themselves, which is a nice compromise if you want just enough to satisfy the craving, but not so much that you're going to get sick of it. Boston sees much lower temps in the winter also. Seattle is very mild for a place so far north, and a lot of people like that, despite the constant grey skies. I remember it being very uncomfortable in Boston when it got above 85 or so in the summer. Seattle again is milder, although they get occasional freak heat spells like the one this past summer when they broke a few records with temps well above 100.
As far as things like the "Seattle freeze"........there are gonna be nice and nasty people anywhere you go. You get as much out of relationships as you put into them, IMO. It just takes time, and you can't make the mistake of getting discouraged early on.
It's a tough choice, but both are great towns. Good luck!
I've lived in, and have relatives in Boston, and I live in Seattle. For me it's Seattle hands down. While Boston has better transportation, chowder, and pizza, Seattle is much cleaner, much safer city. as bad as Seattle drivers can be, Boston's are a lot worse. Seattle has a few neighborhoods that are less than savory. Boston has wide swaths of dangerous ghettos. Boston has a lovely arboretum, Seattle has a lovely arboretum, and many neighborhoods full of trees.
Dangerous Ghettos? Dude Boston is one of the safest major cities in North America.
There were only 63 murders in the Boston metro area in 2008 (2008 murders in Boston - Boston.com) and the majority of those are concentrated in two neighorhoods. So if you mean TWO neighborhoods are alot, then I guess you are right.
I haven't really seen "wide swaths of dangerous ghettos" in Boston either. I think he was probably here in the 80s. Now most of the ghettos have been gentrified.
Boston and Seattle crime wise are virtually identical. Both are quite safe when compared to general U.S. numbers. It's important to compare not just within the city limits but the MSA as Boston is unusually small in its city limits due to it inability to annex neighboring towns.
Table 6 - Crime in the United States 2007 (http://www.fbi.gov/ucr/cius2007/data/table_06.html#b - broken link)
The 2 cities are quite even. It is a tough call. I like the history in Boston and the nature around Seattle. So, I think it boils down to personal preference.
Seattle has a better skyline (similar building number and heights, but Boston's financial district is pure ugly and the Back Bay skyline does not integrate well into the city). But the skyline is the only thing Seattle is better than Boston. For all other aspects Boston wins hands down. Seattle is very overrated on this site. Its downtown is good but public transportation is way behind. Even LA, Atlanta, Dallas are way ahead of it in terms of rail transit. It is a joke to compare with Boston which is very mature in that aspect. Other aspects, history, walkability, architecture, museums, popularity, theater, Seattle just doesn't compare.
UNLESS you cannot handle the gray skies. It's not so much the rain -- it's the GRAY sky month after month. If you have any depression problems, Seattle is not for you.
Seattle is really different from Boston, so it's silly to say that the skyline is all that Seattle has over Boston. The landscape and backdrop of the city, along with the rather progressive fun over there can be really attractive, too.
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Dude Boston is one of the safest major cities in North America. 
Seattle/Boston
