USNWR doesn’t directly consider location. The referenced west coast universities are certainly not ranked poorly. I do think public colleges are underranked due to USNWR methodology, but the highest ranked public colleges were ULCA and UCB, rather than east coast schools.
I don’t think Pomona in #4 and CMC in #6 is a big anomaly, suggestive of a bias against west coast . However, Pomona never ranks as high as Williams. I believe Williams has been ranked 1st on the LAC list during each of the past 17 years. It’s more that the methodology favors Williams than a coastal bias. There are plenty of good east coast LACs that are consistently ranked below both Williams and Pomona.
Stanford does usually rank below HYP, and I explained the reasons for that earlier in the thread. I think a big part of it is Stanford’s popular 5/6 year co-terminal masters program, which hurts their graduation rate. If HYP had a similar number of co-terminal masters students, they would probably also rank lower.