Paperly might do it if you're willing to pay for it. Qiqqa is more focused on organization/reference management but can also do notes and things, and I believe it can be made to work on a Mac with some workarounds. Neither have a cloud service integrated, but you can link a watch folder with any of the usual cloud services if you need it.
Fantastic tool! I wish something like this would exist as a standalone for other apps too. I use Qiqqa (also free and now opensource) and Mendeley (for collaboration only) but right now manual syncing is the only way. Only wish I could create tools like this to sync with other apps also. Also, good luck for your PhD!