As with almost everything in engineering, my answer is... "it depends."
Both are well tested, vetted technologies. Both will take your data and turn it into something friendly for sending someplace. Both will probably be fast enough, and if you're really counting a byte here or there, you're probably not going to be happy with either (let's face it both created packets will be a small fraction of XML or JSON).
For me, it really comes down to workflow and whether or not you need something other than C++ on the other end.
If you want to figure out your message contents first and you're building a system from scratch, use Protocol Buffers. You can think of the message in an abstract way and then auto-generate the code in whatever language you want (3rd party plugins are available for just about everything). Also, I find collaboration simplified with Protocol Buffers. I just send over a .proto file and then the other team has a clear idea of what data is being transfered. I also don't impose anything on them. If they want to use Java, go ahead!
If I already have built a class in C++ (and this has happened more often than not) and I want to send that data over the wire now, Boost Serialization obviously makes a ton of sense (especially where I already have a Boost dependency somewhere else).
