I bought my Charge from Costco. After about a year the charging port stopped working. I took it to the VZW store, they checked it out, then dropshipped a new phone to me. From my experience, it doesn't matter in the slightest *where* you buy your phone. If it's a VZW phone, they deal with it.
I believe you had time on your side. You also probably didn't mention that you purchased the phone from Costco and not the Verizon store. If you had just purchased the phone from Costco and needed a warranty replacement and told the people at Verizon you bought it elsewhere, they would have told you to contact the place you bought the phone from.