I've seen it go both ways between 4.88/5.13 with NSG and 35's. I believe
@pc1p said he would do his 4.88 if he did it over again. He reused his 5.13 axles from his parted out 5 speed TJ which is how he ended up at 5.13. I've seen a lot of love for both setups and not much hate for either.
The 5 speed is very popular with 4.88/33 and 5.13/35. Considering those setups, with a 6 speed I would likely do 4.56/33 and 4.88/35 with the NSG myself since the overdrive is about 1 gear ratio step lower. Mainly for the 3000-3200 rpm cruise for 75-80 as opposed to 3200-3400 for 75-80. Not that I think either would be a bad choice, just some slight pros and cons. Probably also depends on how fast you drive and where you drive.
I chose 4.88 for 33's with the 5 speed myself. I could have done 5.13 but I just don't need that much gear and at a certain point there is a diminishing return in noise, vibration, mpg, etc.