It's hard to tell, frankly. ParadisEO seems to be very active, and is a pretty large library encompassing various metaheuristics besides GP. Note that it is a superset of the EO library. OpenBEAGLE is nice, but it hasn't been updated since 2007. Watchmaker is very good and active right now, but it only has a proof of concept implementation of GP for now. There's a plethora of libraries out there and rather hard to tell which is the best one. And it's not very hard to roll your own GP, so keep that possibility in mind.
