"I've been wanting the EOS 6D for awhile now."
If you run across a store that is offering a deal much "better" than these, run do not walk away from them. These two sources are extremely good and trustworthy.
Do update your LR as the newest version has some great tools. And, IMHO, the EOS 6D will run circles around a D3100. Big improvement and of course you now can use Canon glass.
With a bit of hunting around, it's possible to catch a deal on a camera that might reduce the price by $100... sometimes $200. You can often find the 6D (a $1900 list price body) for $1800 or $1700. Sometimes you can even find it slightly less than that.
But $1000 for a $1900 list camera is unrealistic.
It's a good idea to limit your list of stores to places that have reputations that the community of photographers can trust.
An easy way to check for problems is to do a Google search, type the store name (or website name) and follow that with a word like "scam", "rip-off", "reviews", "problems", or "complaints".
In the case of your store... numerous such page hits come up on other forums, blogs, and elsewhere indicating reasons to be extremely concerned about this merchant. As the saying goes... if the deal seems too good to be true... it probably is.
You can buy the 6D either as a "body only" or with a kit lens. When you purchase it with the "kit" lens, the most common configuration is the Canon EF 24-105mm f/4L IS USM - which is actually a very nice lens. It retails for $1150 by itself. But when you buy the lens as a "kit" with the body, it increases the price of the total package by about $600.
You can find Canon's full list of "Authorized" dealers here: http://usa.canon.com/CUSA/assets/app/pdf/dealer/CanonAuthorizedDealers.pdf
This list changes regularly.
One more thing ... and this may be important to you. Many of the dealers will offer items marked as "USA" or "North America" and others marked as "Import" for the very same item. The import may have a lower price tag. When Canon themselves imports the items going through proper channels, it's marked as "USA". But there are 3rd parties who will find ways to import the gear on their own -- not going through normal channels -- and then put the items up for sale. These are built by Canon in the same factories, but because of how they were imported, they are technially "Gray Market" items. These items are usually not serviceable (no warranty service... and no service even outside warranty.) There may be exceptions but if you buy the items which are imported directly by Canon for distribution in "USA" or "North America" those items are warranted and serviceable -- no question. My personal feeling is that the "import" is usually not discounted nearly enough to offset the risk. I am not willing to forego warranty and serviceability in exchange for the opportunity to save $25.
There are very good prices for bargain hunters right here at the Canon Store. Search the refurbished cameras.
Also, there are good values to be found locally. You have to use your judgement but if you have good "people sense" you can find both price and convenience.
Among cameras, the 6D seems almost immune to criticism. That suggests excellent reliability.
You haven't told us what you like to shoot or hope to shoot with a new set up but considering you'll need a good lens just to get started the 6D / 24-105 L IS is what I'd recommend as the starting point. (assuming you are changing systems). The 24-105 is versatile & sharp making it a very good kit lens.