Why are you so concerned about speed? Do you know right now that you'll have difficulty meeting a performance target on reasonable hardware?

Depending on what you're doing, Python may very well be faster than Java. I've done a lot of work with NumPy and found it to be both faster and safer than third rate roll your own numeric libraries that so Java programmers like to write. I've also had good success with Pyrex/Cython.

Assuming that run time performance won't be the determinative factor, your decision will probably come down to libraries and aesthetics more than anything else. I'd go with Python since I think it would allow you to iterate faster, but that's a very subjective decision.