Does the quote include removal and replacement of the damaged studs? You have to consider that the prices you will find on this site and others for exhaust manifold gasket replacement assume that the job can be performed without any hardware breaking. If the shop has to deal with extracting broken studs, that's extra work, which is, well, extra. Honestly, the removal of studs broken off in a head is one of the least desirable jobs to have to do in a shop. That being said, it is not uncommon to "pad" an estimate for exhaust manifold removal simply because it is the exception, rather than the rule that a job like that will go smoothly. I would recommend asking the shops if they have an estimate on how much they would charge broken stud, that way you will have a high and low range of what the repair should cost.
It just depends on whether the manifold is cracked or if the exhaust gasket is the only leak. If the manifold does require replacement, there certainly can be a difference between different manufacturers of exhaust manifolds. Unfortunately, I cannot tell you who makes the best one for your application. Sometimes the factory part is the best out there, but other times aftermarket units will have updates for known common failure points.