I found some stuff on ebay, but nothing that looked like it would work very well.
Found this but I don't have a 3D printer. I contacted someone locally that does printing, and for $40, they knocked it out for me.
I had to assemble it with a couple of screws and some superglue, but it works really well.

 

Wow that's pretty neat. Someone at Lexus lost a bet only way to explain the horrible cup holders.

 

Looks good. I really need to print one of these.

 

Looks good, I went with a holster for my bottle that sits right under my leg. I rest my arm on the center console alot and I hate repositioning my arm if there's tall stuff in the OEM cup holders haha.

 

I like that! Nice placement.
I have my seat pretty far back, so the bottle in front of the armrest doesn't really bother me.

 

Great solution guys! Probably the only annoying thing in my 06 ES.