If you purchase a PS3 online, you are more likely to get a deal like a rebate or discounted price on it. However, in a store, there may be seasonal discounts or package deals that are worth it, but do not occur as often.
I would suggest buying from a store. Electronic products today are prone to glitches, and by purchasing from a store you can take advantage of their In-Store Warranty as well as the Manufacturer's Warranty. Most online purchases don't offer warranties.
Well the two cheapest options is to either buy a refurbished one in a store or buy one online. Typically online ones won't be much cheaper than local ones after you add on shipping. Try your local Gamestop and see if they have any cheap ones.
If you go to most stores and purchase one new or even used, you will end up paying more than if you were to purchase one online using eBay or some other such site, you just have to be careful of who you buy from and make sure they're reputable.