What is the source of your information that iPhone 5S supplies being limited?
I'd buy from Apple if I were upgrading my contract as well because Verizon charges me tax on the full device price because I have a CA area code. I've fought them for ages on this but they seem to think they're correct. In NC (where I live) you pay tax on the subsidized pricing and not on the full device.
Anyway, I prefer to deal with Apple, personally. Also, if there is a stock issue, Apple will have iPhones first normally.