It's a hard choice. Anyone who uses Box2D will say it's better whilst people who use Chipmunk will say it's better.
I think it ultimately comes down to which you like more. The "liking" can come in many different forms, from the languages they are both based on to functionality found within.
Personally, I like Box2D.
I find it to be a more established engine. It has a larger community, and thusly it's easier to find support and examples for. It's also based on C++, versus Chipmunk being based in C. I like C++ more and find it easier to work with in some cases. You can get screwed over with memory allocation easily, but if you take care of your code you'll be fine. Another major influence is that I really don't like the way Chipmunk's code looks. The "cp" prefix throws me off, and the code itself doesn't look that beautiful. While Box2D takes time to get used to, as it definitely is confusing, it's easy to work with after some experience.
Then again, I'm a Box2D guy... So everything I said is biased. I'm sure a Chipmunk fan can walk in and disagree with everything I've said.
Again, it ultimately comes down to what YOU like. Try both. Create example projects for both engines, look through the test and example files. Search for tutorials: Which engine has blogs/articles that might be able to help you out the most? Try to see yourself typing that code out yourself: Is it comfortable? Can you invision yourself writing that from scratch?
Just play around, and you'll find the engine that's right for you.