I far prefer reading on my Pearl eInk Kindle to reading on my iPad, phone or desktop computer - it's easier on my eyes after a full work day spent staring at a backlit LCD screen. I'd go as far as to say that while I much prefer ebooks to paper books these days, I'd read a paper book (provided it's one I can physically hold open and that has a decent sized font / line spacing) over reading the same book on the iPad.
Other people have different preferences. I preferred my pre-Pearl eInk Sony 505 to reading on the 1st generation iPad, too (although I find the Pearl screen Kindle head and shoulders above the Sony's screen); a friend of mine switched from her Sony 505 to 1st generation iPad and LOVES it and doesn't want to go back to eInk at all.
The easiest way for you to determine which works best for you is to read a book on each on your devices and see whether it makes a difference!