When sending a portfolio of art to a collage what is the best medium to send it in?

Rather than trying to determine what is generally preferred, you should carefully read the submission guidelines for each school, scholarship and competition you enter. These are all highly competitive endeavors, and the first "cut" in judging is the elimination of anyone who can't follow instructions. You should be working on original art right now, and as the time approaches to submit your portfolio begin working on getting high-quality photos of your art. Though each program is unique, it is generally a good idea to include examples of directly observed, representational drawings and paintings, because these demonstrate raw aptitude and ability.