Today I read an article on note taking. In it they commented when students take notes using handwriting, they actually remember the material better than if they typed it. This reinforces something I read during my Master's thesis, they said that handwriting is the kinesthetic part of reading and there is a connection between the hand and the brain. So if handwriting words and letters helps reading, it only makes sense for learning material in general.
This changes my idea about note taking apps. In the article they mentioned that today's notes usually include media/recordings, diagrams, graphic organizers, pictures, written materials, so if you put a note taking app on the iPad, it should allow the students to utilize all of the above. There are some suggestions in the app but I prefer going after apps that can be used independently and do not require you to access the internet in any manner unless you choose to. I do not always have proper access to internet at school.
After a quick search I found inClass, Evernote, Penultimate, Supernote all are recommended. I would recommend you check these and others to see which one works for you.