I just got a 2017 (in my signature) and it's got the 3:31 rear end, and it's not locking, or even limited slip... It's the truck that I could find and afford mind you. I'm not going to campaign for my set up. I do not have experience towing with the other ratios... AND... I've only towed about 300 miles with this setup so far...
With those 4 million disclaimers stated... I can not believe how much better this truck tows than my 2010 5.4L did. My trailer is at least 8300# (Dry/Fantasy weight)
Back to the truck... This engine paired with the 6spd tranny... It's an amazing difference in experience. I guess in short (and other opinions may vary widely) I would not shy away from the 3.31 if the rest of the truck was want you wanted ( you said looking used)... If I had the budget to order whatever I wanted, well.... Haha..
Anyway - just one Man's (limited) experience with the 3.31 - take it for whatever. :) I loved my old "Blue Monster", but, I don't want it back! :-)