One way to go is to either use a mandrel, like a gauge pin or just some round stock, that has the same diameter as the cylinder and indicate off of that, with your fourth jaw out of the way. If you don't have such a properly dimensioned piece of bar stock laying around you could just index off the inner or outer jaw faces themselves.
Clamp the cylinder in three jaws of your four jaw chuck, centered by eye to the best of your ability, with the cylinder set deep in the jaws so you can get the tip of an indicator onto the lip of the jaws. Move the jaws as needed to bring all indicated readings to the same number. Back one of the opposing jaws off the very least that you can and still move the cylinder, then bring the cylinder back up to the front of the chuck jaws where you want to work on it, then screw that slightly loosened jaw back in just the amount needed to clamp back up and then bring the fourth jaw in to clamp onto the steam chest bulge. You should be good to go at that point.
Hope that helps settle the mud out a little bit.