I think a good criteria is your needs and intended use.
The GX470 (a Land Cruiser Prado w/ VVTi V8 & 5spd auto) is a "Land Cruiser Lite". It is better on-road (smaller, faster, more agile) while retaining most of the offroad capability.
You are also gaining the air rear suspension, elec adj shocks, DAC, HAC, VSC, ATRAC, and if you are really lucky you found a model w/ KDSS suspension (if you did, i'd take that in a heartbeat).
I believe the first 2 rows are actually larger on the GX in key dimensions, while the 100 has better cargo/3rd row. Altho numbers don't really mean much... actual seat time does.
Also the 100 is beefier in key areas such as the rear axle, suspension. The GX has a coilover IFS, while the 100 is saddled w/ torsion bars.
I have read several direct comparos that favor the 100's better feel and notch up in interior qualities (same yr trucks). 100 has a larger aftermarket. If you offroad a lot, between the two, the 100 would be better I believe.
The rear door (GX) or split tailgate(100) may also factor into your decision process.
The Lexus dealerships are certainly a cut above if you have it under warranty or use them.
Since the GX costs more, you should figure out if all the above are worth it.