It's almost the same. If you're goin' the stalker way some bosses will be easier then other, and aproximately the opossite for the hunter. After all it's not a lifetime decision as the game is flexible enough (at least in this manner) so you can change your specialty whenever you want. you can't only change the class of the hero, i.e. to became a warrior or mistic. At the upper tiers redistribution of the skills point, thus rechoosing the specialty, is a common trick. So, my advice is to take whatever your gut say.
Also keep in mind gaining exp. for different weapons. This can add up to 22% boost to the damage you deal. Sometimes this little bits make the big difference when you're in front of the legendary or epic leader.