Personally I found Marmoset 3 the best one so far. I used xNormal (Free), 3dsMax Substance and Knald. If you are on a tight budget but can afford substance, it might be the best bang for your buck, since you get the texturing suit as well as their baker which is pretty good aswell.
I second Marmoset. You can assign your high and low poly meshes to baking groups, so you don't need to explode your mesh. Substance Painter has a 'bake by mesh name' option, but I've never been able to get this to work for some reason. Marmoset Tool Bag also has a preview bake, where you'll kind of see what your bake will…
I'm biased of course, but Toolbag is the best baker out there. @Ashervisalis covered most of the important bits. Toolbag shows a real-time preview of your bakes, and has tools to correct skew and cage errors in the viewport. This makes it very easy to diagnose and fix problems. Bake groups (which can be set up via name…