Well, you are correct in your assesment that cert's do not help programmers. Although people with MCAD's might disagree with my opinion.
A few questions:
1) Does your schooll offer a combined BSCS/MSCS that you can get in 5 yrs, vs the traditional 4yr BS followed by 2yr MS?
2) Why do you want to get your masters? The reason I ask, in my opinion as a manager and fomer recruiter, a MSCS has a tendency to make you over qualified for entry level positions and underqualified for most research positions (which typically require a PhD). During that those 2yrs pursuing a MS, you could be in the workforce earning $45k - $60k/yr, plus 2 yrs in to hitting that magical mark of 5yrs exp. Its just something to think about.
3) Unless you plan on working part time during college in tech support, I would concentrate on making better grades or even better, pursuing an internship/co-op.
My 2 cents worth