I go with what works for me, as simple as that sounds. I play pretty lightly, but dig in sometimes, so I need a good amount of output (pickups are usually as high as I can get them) without getting the noise you're describing, when the string hits the pickup. Also, some pickups have a stronger magnetic field than others and can mess with how the string is moving, giving it a weird, almost echo or chorus type sound. If you get that, definitely lower the pickups. If you're comfortable doing your own setup, you can experiment until you find the right balance for you.
I tend to play mostly active basses as of late, and active pickups (VFL's in particular) have weaker magnets than passive basses, so you can raise the pickups pretty high. I have maybe 1/32-2/32" in between the bottom of the string and the top of the pickup, when the string is fretted at the last fret. It makes for a good amount of output, and very high sensitivity, so my playing is based on what I do, and not what the bass is dictating, if that makes sense.