Are bosses harder as a stealth-based character?

The difficulty should be quite the same but that also depends on the boss fight.

The main advantage of playing as stealth character is that you may have much more ammunition for the boss fight left than a combat oriented player. Combat based augmentations are an advantage in boss fights but they are not overpowered, so for example the Typhoon Explosive System won't kill bosses. And also stealth based augmentations can be very useful for boss fights like the vision augmentation to see/track cloaked enemies (if the boss uses cloaking).

I consider the Dermal Armor augmentation as the most useful combat based augmentation for boss fights reducing the damage you receive and with the EMP Shielding upgrade preventing energy losses by EMP and electricity. This upgrade may be also an option for stealth characters.

I'm doing a stealth/pacifist run, and I don't feel that I've been overly disadvantaged by my augmentation choices. In fact, some of the stealth augmentations are quite useful during boss fights. Cloaking, in particular, is great: it's a lifesaver when the boss has you cornered and there's not adequate cover to sneak past him or her.

The biggest disadvantage I've noticed so far is that by not having any strength augmentations, I can't carry around a big cache of powerful weapons and the ammunition they require. There's extra ammo available once you engage the boss, but it does make things tricky as you'll have to scramble for a new gun when you run out.