This is a question we get all the time at LOJ, and it is a tough one to answer. A lot of it comes down to your long term goals for the car and your starting budget to get the project done.
Yes, 90% of the time the customer will be able to find a used iron or aluminum block truck engine for less money than an aluminum equivalent. For arguments sake, I'm going to make a few cases so that you can see which category you're in to help make the best decision possible.
ONE KEY ASSUMPTION! Your project REQUIRES you to convert the truck engine to a "car" configuration. Because of clearances you need to run a car Intake Manifold, Accessories, and Oil Pan.
Case #1 - The 5.3L Truck Motor (Gen 3 Iron LM7 or Aluminum LM4)
The LM7 is likely the #1 go-to budget "LS" engine the cost conscious swapper will go to. They can be had routinely for $500 or even less, which makes them an attractive option when budget is an issue. Keeping in the "budget" theme, lets look at the least expensive options available to change this engine to a car configuration. The aluminum LM4s pop up for $800 from time to time as well.
Intake Manifold: Since all 5.3L motors, Gen 3 or Gen 4, have cathedral port cylinder heads, the least expensive low profile intake manifold available for these motors is the factory LS1 intake. These intakes can regularly be found for $300-400 with rails, injectors, throttle body, and sensors. Sometimes you'll find them for less, but I'm basing these prices off of what I would most often see on the used market as of mid-2016.
Additionally, you'll need to buy a Corvette/CTS Crank Pulley (Harmonic Balancer), Balancer Bolt, Water Pump, and Accessories. A good price on a new water pump would be $150, and a Balancer and bolt could be had for about $150 as well. Last up is accessories... prices can range wildly here, but expect to pay at a minimum, $300 for the brackets, hardware, water pump, alternator, belt, pulleys, etc.
As you can see, the true cost of running a 5.3L engine is more like $1500, and that is if you decide to leave a stock truck cam in it. If you decide to do even one of the most inexpensive cam swaps out there, and LS6 cam and spring package, you're adding another $400 to that price. As you can see, the price escalates to the $2000 range rather quickly. If you're running an aluminum 5.3, you'll easily pass $2000 just based on the price premium the aluminum motors bring.
When you start to consider that genuine LS1 engines are starting to pop up in the $2500 range, you have to start thinking about the real benefit of running a 5.3L engine in these applications. The strongest case i know of is if you're going to boost the engine. If you blow it up, replacements are cheaper and easier to come by than real LS1s, and many would argue that the 5.3L, with its iron block and increased wall thickness and gasket area between the cylinders, actually makes for a better boost platform.
Case #2 - The 6.0L Gen 3 Truck Motor (LQ4/LQ9)
The LQ4 and LQ9, for many years, were the go-to engine for swappers, the de-facto engine of choice when it came to dollars per HP. There 6.0L engines, for all intents and purposes, were exactly the same except for their cam and compression ratio. The LQ4 had a slight dish to the pistons, keeps the CR in the low 9's. The LQ9 has flat-tops that get the compression up into the mid-10s and a LS1 cam stock. I'm starting to see LQ4s in the $1200-1600 range and LQ9s in the $1500-2000 range. Sometimes much more, and sometimes less for high mileage motors. Lets just say for arguments sake that you can get a LQ4 for $1400 and an LQ9 for $1750.
Taking the same approach as above, a LQ4 with its stock cam would cost $2400, and $2800 with an LS6 cam. Want to step up to an LS6 intake and you're up into the $3000 range. The LQ9 would be $2750 with the stock cam, and that's ok since its an LS1 cam, but won't make great power.
In either case, you can most certainly get an LS1 for that price, which begs the question if the modest increase in displacement and 80lb increase in weight is worth it.
Again, if you're going to boost the motor, the Iron has its advantages and those can't be denied, but it isn't as attractive as option as it once was. If you put a true LS6 intake on it and an LS6 cam as well, you essentially have an engine that will out-perform a stock LS2, but that will bring the price to close to $3500.
Case #3 - The 6.0L Gen 4 Truck Motor (LY6)
The LY6 is the newer kid on the block when it comes to "budget" motors, but the prices have been dropping a lot lately. I regularly see these motors in the $2000-2500 range. The hidden beauty of these motors is in the cylinder heads. The stock heads on the LY6 are the same as LS3 heads. The only difference is that the LY6 doesn't share the lightweight sodium-filled intake valves. Still, this motor responds VERY well to a simple cam swap. These motors also come with Variable Valve Timing (VVT) from the factory, but do not have Displacement on Demand (DOD).
The VVT may seem like a nice benefit feature, but for space restrained applications, it actually isn't. The VVT solenoid protrudes too far from the front timing cover to run a Corvette or CTS water pump, which means it needs to be eliminated to run one of these pumps and accessory drives. That costs money, which adds to the cost of using this motor. Coincidentally, it also explains why the Corvettes never had VVT.
So, using one of these motors is going to be more money than a LM7 or LQ9, but it will also make more power than either of those with just a cam swap. Lets say $2250 for the motor, $1000 for an aftermarket cam/spring package with VVT delete parts, and $700 for a brand new LS3 Intake/Rails/Injectors/Throttle/Sensors. That brings the price up to $3950. This is still thousands less than a true LS3, making this one of the cheapest ways to get into a Gen 4 motor. These prices are also based on a NEW intake manifold package, a much newer and likely low mileage motor, and an aftermarket cam and spring package, which means reliability and power will both be better than any of the other options mentioned already. Also, the price is dangerously close to the LQ9 with LS6 components price, which makes this, in my opinion, the better option if you can spare the few bucks extra.
Conclusion - For Now...
It is, in my opinion, a genuinely tough decision to make when trying to pick an engine for one of these conversions. A savvy swapper can likely find deals on some of the parts I mentioned that were needed to convert the truck motors, but honestly, the same savvy swapper can find a good deal on an LS1 or LS2 as well... so take that with a grain of salt.
My recommendation? Think long and hard about what engine you want to run and what your project goals are before you jump into anything.