Harvard Extension School’s tuition is much lower than Harvard’s. However, it is still costly considering the three required classes, as compscigrad says. Here is the page on tuition and total cost: http://www.extension.harvard.edu/tuition-enrollment
Harvard Extension does have financial aid (after those three classes), but that might not apply to you.
Of course, attending HES also includes living in or near one of the most expensive cities in the country.
Will your employer cover those three classes? Admission is approved if you get B’s on these classes. It is not as selective as Harvard University’s undergrad or grad programs that are not part of Extension. Chances are, you’ll get in.
But is it the best way to go?
Tufts does have a great program, with a lot of flexibility, and there are fellowships that pay tuition and involve teaching. If you are doing a part-time program, not sure if those are available to you though. In any case, your employer is paying…
I would also look at Northeastern, BU, Brandeis and UMass Boston.
Why are you getting a master’s in CS? Many in that field seem to continue with a BS only! Does your employer want you to do this? Are you aiming for a PhD and teaching? If so, a school with funding for teaching might be better.