I have one bad grade on my transcript and I'm thinking of applying for MS CS programs at top US Graduate schools. How badly would my chances be hurt?
There's no question it will hurt.  You already know that.  How much it hurts depends on where you're applying and whether it's to a master's or PhD program.
Top PhD programs could fill every spot with students who only have 4.0 (perfect) averages.  The reason they accept students with less than perfect averages is because they also consider your LORs (letters of recommendation) and your essays, especially, your SOP (statement of purpose), which may be enough to overcome that one bad grade.  Lesser programs accept less.
If you're applying to a master's program, admissions are generally more accommodating since they don't have to assign a faculty advisor and they know most master's students are heading into industry, not academia.