<p>Don’t worry. Many students, even those coming from prestigious colleges, have little to no coursework in archaeology before starting a graduate program, and computer science is becoming very important in many fields. Lacking a strong background in a foreign language or two might hurt, though. </p>
<p>Staying in New York, you can’t do better than NYU or Columbia. Cornell has a good Masters program, but it’s a bit further away from NYC. SUNY Stony Brook also has an archaeology program, but I don’t know much about it. </p>
<p>U Penn (various programs), Princeton (joint with art history), Yale (MA only), Harvard, and Brown also have excellent programs, but they’re very difficult to get into. Bryn Mawr, Penn State, and Boston U might be a little easier to get into. Slightly further away, GWU and Johns Hopkins have good programs. MIT has a sort of archaeology-engineering grad program that might fit your CS background.</p>