I'll give you my recommendation, but its a bit different than your choices.
First, I personally own the Nook STR, the Sony PRS-T1, and the Nook Color. The Nook STR and Sony both make great e-ink readers. I prefer then Sony over the Nook, but its a personal preference. Neither are rooted, as I like the way they work just fine.
The Nook Color started as reader for my wife, but I first rooted it, then I overwrote its entire OS with CM7. It now functions as a great android general purpose tablet. My suggestion is to go this route. It would cost you close to $100 more, but for that money you get great functionality as a tablet, and color screen. I think you will enjoy the color screen for your mangas (they do come in color, don't they?) and you can take your pick of a number of PDF viewers that work very well on it. Also, web browsing is great on the Nook CM7 tablet.