Following are some of the best universities in Untied States for MS in Biotechnology:

University of Wisconsin
http://www.ms-biotech.wisc.edu/

Northeastern University
http://www.biotechms.neu.edu/

Johns Hopkins University
http://advanced.jhu.edu/academic/biotechnology/msmba/

Georgetown University
http://biotechnology.georgetown.edu/ms-degrees.html

William Paterson University
http://www.wpunj.edu/cos/biology/grad.htm

Roosevelt University
http://faculty.roosevelt.edu/watson/index_files/Page572.htm

The State University of New Jersey
http://careerservices.rutgers.edu/biotechnology.html

The University of Rhode Island
http://www.uri.edu/prov/degreeprograms/grad/biotechclinical.html

I have mentioned a link to respective Graduate Biotech webpage of each and every university below their names. You can find more information on Bio-tech program they offer by visiting the pages I have provided.