I know I'm a homer, but I think Boston does "beautiful" better. I prefer the redder color palate of the inner brick neighborhoods and it's a greener landscape in general with all the trees and parks. It also is quite hilly (about half that of SF) and sits on the confluence of 2 rivers emptying into the harbor.
It's really close and SF might look a bit more majestic from a pulled out view, but I lean Boston, the "Athens of America" because of its inner brick neighborhoods including Beacon Hill, North End, Back Bay, and South End. Some other neighborhoods, such as "Southie" actually bear major resemblances to SF neighborhoods.
I'll put SF at #2. Philadelphia could have challenged if it had a better landscape surrounding it. I guess you could also look at smaller cities like Savannah, but I'd prefer to stick with "big" cities.
Beacon Hill is probably the single most beautiful neighborhood in the country.
Beacon Hill by
Daniel Tinkler, on Flickr
North End is right up there.
IMG_1214-HDR by
Phil, on Flickr
Looking down on part of the Back Bay neighborhood from the Prudential.
Boston view from Prudential Tower by
Larisa, on Flickr
The unheralded but still very impressive South End neighborhood fronting the Financial District.
DJI_0672-HDR by
Phil, on Flickr
Pulled out view from the Prudential observation deck, which offers 3 levels (including an outdoor level) and 360 degree views. Every time I go up there I am certain that this is the most beautiful city in America.
Moonrise over Boston by
Terry Donovan, on Flickr