Yes, there is a significant difference between eastern and western Redwood City, but that's not to say there aren't good pockets on the east side. Lenolt as you go west from Woodside Road is good, and Friendly Acres is better than it used to be. Bair Island is pretty cool too, but I don't think you're talking about there.
As for Pacifica, East Sharp Park is basically San Bruno and gets horrendous fog. I don't know if it's in the airport flightpath but it may be. The southern side is much more desirable.