If you buy a new USA lens or camera and you live in the USA, it doesn't matter where you bought it.
That is really the only thing you need to make sure of, since Amazon is not only a retailer but a front for other retailers with differing products.
If you have to get it serviced you will mail it to Nikon not the reseller. I have bought USA products from Amazon, B&H and other places and never had any problem with returns and as I mentioned Nikon is where you send repairs to (for example my D7000 bought at B&H last November is on it's way to Nikon in Escondido, CA for some repair). The warranty is LONG enough for lenses that there is plenty of time for you to spot a flaw and get it repaired. The likelihood of repairs however, is very low for Nikon lens.
Where you have to be more careful is eBay, but even there if you ask the right questions to the seller before buying, eBay Buyer Protection kicks in if you have a problem with a seller. This happened to me recently with fungus that was hard to spot on a 180 AI, but I have bought lenses before and since and never had problems.