The tweeters should be at or near ear level. Usually when I have been using the computer for while, I find myself slumping down into the seat, which puts my head well below the tweeters. With my present speakers, this doesn't really hurt the sound too badly, but I have used speakers on my computer desktop that really sounded awful when I listened too far down the vertical axis.
If you find the tweeters a bit higher than your ear level, one thing you can try is simply turning the speakers upside down, and seeing how it sounds then. It may lead to an improvement since the high frequencies tend to be more directional than mids or bass.