I second Harry.
I'm a researcher and use my iPad3 extensively for work. iAnnotate, GoodReader and PDF Expert are all excellent annotation apps and they sync via dropbox. I used to have an iPad2 and while I'm not someone who typically upgrades every time a technological gadget comes in a new version, I exchanged it with a 3gen because of the retina display. When you are reading academic articles/pdfs for several hours a day, the screen resolution makes a difference. The screen size allows for comfortable pdf reading, IMO - I don't have to zoom in to read.
In addition, I also use Sente for bibliography management (this syncs with my mac), but you can also use Mendeley or Papers.
My recommendation is to definitely go for a tablet rather than an e-ink reader. I've outlined some of the reasons here, in other thread:
I've found that my iPad has greatly improved my academic work flow, and I warmly recommend it. If you can afford it, I'd go for the 3gen.