An important question, surprisingly often overlooked, is how you want to actually spend your time, day by day and hour by hour. In academia, you will immediately be plunged into hands-on science, and your drivers will be to start out on your career by getting results, publishing, networking, and building your reputation with a view to impressing your tenure committee. A career in industry may put more of an early emphasis on your organizational aptitude, people skills, powers of persuasion, ability to strategize and execute to plan, etc.; in terms of growing your reputation, your audience will be the rather narrower community of your immediate management. A somewhat more cynical view would be that in business you will spend seemingly endless hours in meetings and writing plans and reports, while in academia you will spend all that time and more in grantsmanship—in this regard, you must pick your poison.Courtesy MR, David B Searls on Ten Simple Rules for Choosing between Industry and Academia.
Finally there is the elephant-in-the-room question: Do you want to make money, or to help people? This is, of course, a false dichotomy, but many people consciously or unconsciously frame the decision in just this way, and you had best deal with it. Try thinking of it not so much in terms of the profit motives of the respective institutions, but in terms of the people with whom you would spend your career. You should have encountered a good sampling of scientists from industry during meetings, internships, collaborations, interviews, etc. (or in any case you should certainly try to do so before making judgments). If you are left in any doubt as to their ethics or sincere desire to relieve human suffering as efficiently as possible, or if you feel these are somehow trumped by the corporate milieu, then by all means choose academia—but only after applying analogous tests to the academics you already know well.