I use my ipad extensively to annotate pdfs, using both a stylus and the keyboard. I use Sente for pdf management, and Sente and iAnnotate to mark up the articles. iAnnotate is by far one of the best annotation apps for iOS, with GoodReader and PDF Expert as high quality alternatives. I have written about how I use iAnnotate here
and Sente here
In short I think both an iPad and a Nexus would do the job without any problems, and if you use DropBox you can sync your documents to pretty much anything and anywhere.
One thing to consider is the rest of your eco system. For example, if you have an android phone you might want to stick with the Nexus, or if you have a mac or an iPhone you might want to go with the iPad.
If you're doing a lot of reading, the quality of the screen would be another factor. I would encourage you to check out both tablets in a shop, and have the shop assistant show you what a pdf file looks like on both screens. Screen specs are important but they are not always the whole story.
Both iOS and android come with huge app stores, and in terms of pdf reading and annotation I think you will find what you need in both.