Tough call. I have been playing with both Penultimate and goodnotes. I really like goodnotes - as a notes app - much better than penultimate. It is easier to use. It has a better interface and is much more versatile. There seems to be fewer bugs. For example, in both penultimate and goodnotes, you can cut text and move to another place in the document. You can do this in penultimate as well but it oddly leaves behind pieces of the text in original place.
However, goodnotes doesn't synch with evernote and I don't think there is a desktop option. So this is a big mark against goodnotes.