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For the two options you listed, I would get the hitch (trailer tow package) from the factory/dealer ... this just makes sure all the wiring etc. are done ... and under warranty. But I'd probably get running boards/bars aftermarket. Personally, I found ebay to be a great source.
The factory tow package is well worth the money you get the hitch, wiring, trans cooler and heavy duty batt and alternator. Well worth the money. running boards i would say go aftermarket
I agree you should go with the factory tow package. I would also go with the factory running boards, aftermarket won't be much cheaper and unless you know or have a good shop you could get shoddy workmanship. Also beware when you order and make sure it's a Ford option and not a dealer added option.