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The Trek Mamba has the spec you want (although it's a low end Rock Shox fork), and the MSRP is $1019, so you should be able to find it for under a grand.
Giant offers their Talon series, with a model a bit above and one a bit below, but you only get a Suntour fork. Of course, even a bit over your budget, the Talon 29er 0 uses a coil spring Rock Shox, so it's not much better than the Suntour.
Both companies have solid and reliable bikes in the $600 range, but you don't get a huge improvement jumping up to the next level, in my opinion. I have the Trek Wahoo, which sells for about $600, but I upgraded to XO, Avid brakes, and a Rock Shox fork. That route would easily exceed your price range, but if you are handy and shop around, you can upgrade it over time and come out with a better bike. I scored some uncommonly good deals, which resulted in $1,000 in upgrades for about $140. You're not going to get that, but you can certainly come close. I have seen nice Rock Shox on eBay for $200, and complete groups for the same price. So spend a grand, and have a nice bike, or spend $600 and have an ok bike too, but another $400 could turn it into a great bike.
There are other 29ers out there, but these are the two I am most familiar with. If you're not fussy about the label on your bike, Bikesdirect offers a couple of 29ers with better spec than either of the above bikes, priced from $900 to $1300.