I'm doing Singapore to San Francisco r/t in a few weeks, and faced the same question. HKG or NRT?

I chose HKG for a few reasons.

First, I like to settle into a long-haul flight and make it "my space" for as many of the hours I'm traveling as possible. With the NRT connection, you spend a lot longer on the "shorter" flight, and less on the "longer" flight. I'd prefer a quick hop from SIN to HKG and then treat HKG-SFO as my long-haul where I'd bother to take off my shoes, dare to sleep, etc.

Second, the upgrade possibilities (I'm doing NF, not NC, but it's the same basic situation) are mostly the same on the ex-SFO legs. The 747 definitely provides better odds than the 777 for an upgrade on the intra-Asia legs, so the HKG-SIN legs are much easier than the NRT-SIN legs -- I know this one first hand!

Third, HKG is a better transit airport in my opinion. More to do. Easier to navigate.

Only drawback is that the crews intra-Asia are generally (i.e., always) better, so you have more time to enjoy their service on the NRT-SIN leg! But you're virtually guaranteed to be asleep on the way back anyway.