i've done both. both have pluses and minuses. if you disconnect the hoses, and electrical connectors, unbolt the exhaust downpipe from the exhaust manifold, unbolt p/s pump and so on it all comes out together with the manifolds. makes it easier to reinstall the manifolds without hassle while the head is on the bench.
unbolting the manifolds in the jeep is fine to, then you can leave the exhaust together, and remove the intake manifold, then the head comes right out, this is also better if you are by yourself, it is pretty hard to lift the cast iron head and manifolds out together by yourself.