Sentence #2 doesn't mean the same thing as the others. From #1 and #3 I would get the idea that there are maybe multiple new models of Mac computer being released, or maybe the same model is being sold by different vendors, and out of those options the cheapest one costs $1000. Sentence #2 doesn't tell me that, it gives me the impression there is only one way of buying the newest Mac and it always costs $1000.
None of them sound very natural, they're all a bit robotic. #1 sounds very stilted because it's too simplistic in its structure: too nominal, plain SVO and the generic verb "is", there's nothing expressive or spontaneous about it all. #2 doesn't sound good either because it loses too many details. Out of the three I'd go with #3, but it still sounds rather awkward. If you actually need this phrase (not just as a theoretical exercise) it'd be better to rephrase it completely I think. The best way of doing that kind of depends on what you're trying to achieve.
If you're trying to promote the new Mac or at least present it positively, I'd go with "The newest version of Mac computers can be yours for as little as $1000", maybe then clarify what the other options cost and whether this depends on the model or vendor or both. In that case, the idiomatic phrase "as little as" helps you because it emphasises the word 'little' and people will maybe perceive it as less expensive than they would if you phrased it differently (idiomatically, the correct adjective here is 'little', not 'low'). The expression "can be yours" also entices people because it emphasises the pleasure of owning the newest Mac. However if you're trying to be neutral or more negative in your tone, I wouldn't use this phrase because it can sound a bit too smooth and stylised, like "salesman's talk".
If you're reviewing it and maybe being a bit less positive about the price, I'd go with "The cheapest option to get the newest version of Mac will cost you no less than $1000", which has a very different ring to it. It's not overtly critical but there's some subtle emphases there ("will cost", "no less than") that make it sound less positive. For a more neutral option, maybe go with "If you want to try the latest version of Mac computers, the least expensive option comes down to $1000" or "the newest version of Mac computers starts at $1000".
There's a lot of subtle meaning you can add to the phrase which changes depending on which words and expressions you choose, whether or not you choose to emphasise the price or present it in a particular light. Because of that it's hard to give a single phrase that sounds "more natural". There are several ways of saying the same thing in English that sound natural, but not all of them would be perceived in the same way and some of them may sound unnatural or awkward in a particular context. For example "The newest version of Mac computers can be yours for as little as $1000" is something I'd totally expect to see on Apple's website or maybe in a positive review, but I'd be annoyed if a friend talked to me like that because it sounds like they're doing a sales pitch.