Get a keyboard dock. The onscreen keyboard is intuitive but still far inferior to actual physical typing. That and your iPad in your backpack are a lot lighter and take up a lot less space than lugging around your laptop and possibly your charge. As for actual apps, Penultimate is good for freehand notes, especially if you get a stylus. You can also of course get Pages. I haven't tried Evernote but I hear that's good too.
Don't worry about if other people in class use them. If they do, cool, if not, you'll be the cool kid. Really, in university, nobody honestly cares how youtake notes, if you show up, sleep in class (unles you snore of course 🙂 ). Good luck!