Nobody can really answer this for you because it depends on your budget and what is available near you. I got my LQ4 on eBay because it was super clean, low mileage, and fit my price range and plans for the truck. The LQ9 is higher compression and generally considered better for NA builds, while the LQ4 is generally considered a better candidate for boost (and cheaper). The 4.8/5.3 should be cheaper than either and might be readily available in your area (try Craigslist).
Personally, I don't have the patience or interest to screw around and modify a factory harness to work so I bought my harness, DBW setup, etc from PSI and it was by far the best investment I made for the swap. A little pricey but I plugged the whole harness in in about 15 minutes and fired it up. It looks stock, and I don't have nasty wires running everywhere under the hood. Unless you have the time or inclination to spend hours on wiring, I would highly recommend investing in a pre-made harness. PSI was great and I was able to tailor it to my exact specs for the truck.
'04 Hemi QC - H/C/I/bolt-ons/tune - Sold
'70 C10 SWB Stepside - LQ4/4L65E