IMO, there are two reasons why shoes/boots with heels can be uncomfortable.
1) Because the shoe doesn't fit (too small, too narrow, instep not right, etc.). In this case, you need to find a style or brand that fits your foot, and the height of the heel does not impact how they fit your foot.
2) Because of the slope of the heel, i.e standing on yout tiptoes (3", 4" 5", etc). In this case, a shoe can fit your foot, but if the heel is too high for your comfort, then it doesn't really matter how well the shoe fits, does it?
As for finding a high heeled boot that is comfortable, I am guessing that you mean a boot that fits your foot independent of heel height. Right? Because a 3.5" heel is a 3.5" heel regardless of brand.
I love many of Stuart Weitzman styles (ESPECIALLY boots), but my experience is SW runs narrow and is not comfortable for my feet. However, I do have one pair that are my all time favorites.
I would consider brands that are not quite as designer, but nonetheless offer many cute and sexy styles of boots and tend to be more comfortable for the masses than many designer styles. Nine West, Charles Davis, BCBGirls all have a great selection of boots with heels that may possibly fit your foot better. Worth a try.