JavaScript: The Good Parts has passages like this:
The new function object is given a prototype property
whose value is an object containing a constructor property
whose value is the new function object.
... whereas Eloquent Javascript is written in English.
[Edit: To be fair, Douglas Crockford does write in the preface that the book is dense and may require multiple readings. He means it.]
I'm the author of Eloquent JS, so I'm far from unbiased, but the main difference in my mind is that The Good Parts is very spartan and extremely prescriptive in what you should do and, especially, what you should never do, whereas Eloquent JS tries to actually be attractive to read and have a much more open and enthusiastic mindset towards what programming is.
My favorite quote from the Good Parts: "if you want to find out more about the bad parts and how to use them badly, simply consult any other JavaScript book"
To be honest. I've seen way, way worse. He is very, very, VEERY arrogant - if you don't put space before and after an operation sign, you are an idiot. But the man earned it, somewhat.
I've seen people that are that arrogant and have delusions of grandeur. They are the poison, really.
They are not really comparable, Crockford's book is for programmers who want to use JavaScript and do it 'The Right Way' TM. Eloquent JavaScript reads much more like a story that happens to teach basic programming concepts, which happen to use JavaScript. It could be read both by an experienced developer and a someone who wants to dive in with no programming experience. The Good Parts would be useless to a beginner.
For someone who has rarely if ever programmed (or just done basic HTML/CSS) I recommend Eloquent JavaScript. For experienced programmers or someone who has been hacking JS on their own for a while, but wants to improve, I recommend The Good Parts.
You can learn a lot from both, but they are aimed at different audiences, IMO.
[Edit: To be fair, Douglas Crockford does write in the preface that the book is dense and may require multiple readings. He means it.]