I actually like Circus Ponies Notebook on the Mac and the iPad. The ability to create an outline, tables, and freeform drawing is indispensable.
Syncing isn't quite perfect yet. I have to drag and drop Notebook files with iTunes so that I can use it on my iPad. No over-the-air syncing...... The blogs did state that they would get DropBox syncing soon and will explore iCloud syncing when it is officially released.
To complement your iPad, I'd recommend a nice case and even a bluetooth keyboard.
Here's a cool iPad case/stand:
http://www.youtube.com/watch?v=AvzuYPu68yA
There is an iPad generation 1 and iPad 2 edition available. It's an interesting stand with variable positions to prop up your iPad. The case/stand also swivels out just enough so that the backside camera is not blocked.
Then when I really want to do some heavy duty typing, I might suggest the Matias folding bluetooth keyboard:
http://eshop.macsales.com/item/Matias/FK304/
I'm starting to learn to use mind mapping as a note taking tool.
I just bought NovaMind 5 because it allowed me to view my thoughts in both mind map and outline format simultaneously.
www.novamind.com
Here is a NovaMind 5 video tutorial on how to take notes or brainstorm in NovaMind 5.
http://www.novamind.com/blog/2011/tu.../brainstorming
For the iPad, iThoughtsHD is available and can use DropBox to sync with NovaMind, Mindmanager, and a lot of other mind mapping programs.
Mind mapping is another way to take notes and might help you out.
An alternative idea is to get one of those new MacBook Air (particularly the 11.6" edition). The 11.6" MBA is just a little bigger than an iPad so it won't be as heavy as a MacBook or MacBook Pro. Then you can use Circus Ponies Notebook on the MBA and don't have to worry about syncing Notebook files.