Slee off road has one of the best write ups of year and model differences (LC vs Lexus LX470)
If you haven't already check out the 100 series forum on ih8mud it's a huge resource for 100 owners
I talk about a few reasons on this vid but don't go very deep into it.
Here are the main things to consider in my opinion.
2000 Front differential was changed from a 2 pinion to a 4 pinion unit. The 2 pinion was prone to breaking
2000+ have A-TRAC (Active Traction Control) which is great but some early models have a rear locker
2003 gets more Horsepower
2006 and 07 for the land cruiser get AHC is an option
The lexus is nicer inside, there are way more of them in the US so easier to find, but some mods are designed for the cruiser and not perfect on the LX, Most importantly all 98+ LXs have AHC
Some people like AHC but it can be a maintenance pain in the ass and if you want to upgrade you'll need to get rid of it. Not impossible but something to consider.
RUST - You will find some that are ate up and they can require a lot of maintenance and tough to work on.
I would say take the first one you find with little to no rust underneath. No AHC is a big plus and stick to a 2000+ to get ATRAC and the beefier axle. 2003-2005 Land Cruisers are going to be the best overal for technical features so if you can find one with little to no rust jump on it.