Just out of curiosity, if you have all this extra money to spend, why didn't you get a more expensive bike in the first place? You would have ended up with a much nicer bike in the end had you spent the money up front, rather than bought a bike you planned to upgrade and upgraded it piecemeal. Especially after having it for only a couple weeks. No offense intended, just trying to figure out your motivation. I feel like by the time you're done upgrading, well, you'd definitely have had the money for a Giant Yukon FX if an FS was something you'd consider...heck, you might have been close to a Giant Trance or Specialized Camber. Or if you really like that hardtail, you could have gone with a nicer Rockhopper or maybe even a Stumpjumper HT. If you've been thrashing on it for the past couple weeks, it's too late to take it back now, but for future reference, when you buy a bike, buy the nicest one you can afford, and don't plan to upgrade it right out of the box.
Either fork will be an improvement over the Suntour. I'm not familiar with the Marathon, but the Recon is a great fork.
The difference between a cheap fork and a good fork is simply that the good fork actually works. I know that sounds like a "Duh, not helpful" answer, but I'm being serious. Cheap forks either bounce around like pogo sticks or don't absorb anything like rigids. A nice fork will actually do what it's supposed to do and absorb shock. Plus, your adjustments will actually do something, rather than just being knobs on the fork that look nice like on cheap forks, so, assuming the fork has adjustments for these, you'll be able to adjust the rebound, compression, and lockout.