Essentially no difference, they are both using the same exploit. Some people will say that the GreenPoison one will be less buggy but really they are just guessing. I've been running limerain for a few days with no problems at all.
At the end of the day, a jailbreak is a jailbreak. It doesn't really matter where it comes from.
I'm on limera1n beta 4, just checked twitter and GP is now at RC3 and they are awaiting feedback, will check later and probably update, don't like being on a beta, know it don't make much difference but that's just me