I wouldnt deal with them until I was ready to.
By that, I mean I had taken and fully developed all planets on my side of the pirates, then done all the research. Use the pirates as a buffer so that you have time to do things without worry of being hit.
I'd then produce a fleet maxing out all resources, and when all was ready, I'd hit the pirates with everything. 16 capital ships, and 300+ cruisers and frigates, is going to make a mess of any sized pirate fleet.
Then you split the fleet into an attack fleet, and a blocking force, reinforce the ex-pirate base and use it so that nothing can come through to threaten "your space" while you go take the rest.