1st
I'd want to know if both trucks were original owner trucks and what the owner(s) did with them, work/tow, daily drive, weekend warrior etc
IMHO, things to look for would be trailer brake controller, a 5th wheel, helper air bags excessively beat up bed and/or excessive wear around the hitch
2nd
I'd probably want to talk to them about maintenance, it sounds like the LLY has had decent up-keep. If the LB7 is on original injectors you can be pretty certain that a new set will be needed soon...and that's a pretty big job that can be really expensive to have done. You'll want to know stuff like, have fluid flushes been done, if the coolant has been changed and when, if the brakes have been done and when, have the shocks been replaced, have the steering components been replaced (ie pitman and idler arms) and regular stuff like the spin on filter for the Allison, how often the fuel filter was changed and oil change intervals and oil type used.
3rd
I'd want to know where the trucks have spent their life and how the undercarriage looks...rust and/or peeling frame coating is never a good sign
4th and finally
I'd want to know if any aftermarket goodies have been added to either rig, like exhaust, gauges, ANY sort of tune or programmer etc. It's good to know if the owner has put any love or hate into their vehicle, "love" meaning a cool exhaust and maybe an intake or efi-live programming, "hate" meaning a chip or off the shelf box tune like a predator programmer
Ultimately, looking at a purchase between these two rigs shouldn't really come down to power output cuz it's pretty easy to safely get more go juice out of either with a good EFI-Live tune or dare I even mention it, a Banks tune (which is the only tune other than an EFI-Live tune from a reputable tuner that I would ever recommend)
If the LLY has a 6sp transmission I'd say that's a pretty huge bonus and that alone would heavily sway my vote, and for more reasons than just the transmission.
With any purchase choice my bottom line would probably be the condition of the rig and the owners care/maintenance habits, honestly tho, I'd imagine you could find better choices to pick from (not that the two your speaking of are bad, per se)...personally I'd look for a 2005.5 LLY to 2007.5 LBZ with 120k mi on the clock or less, that doesn't have any provisions for or evidence of a 5th wheel