Notes played on the E string usually have a naturally higher amplitude for obvious reasons (it gives you the lowest notes on a typical 4-string, after all!), but if it's too imbalanced, a simple pickup height adjustment should help. Just lower the pickup on the E-string side by turning the screw down. Just a little should do the trick. Slight turn, play notes to test, repeat until satisfied.
Alternatively, the other end of the pickup (G-string) could be too low as well, and you can raise it a bit to compensate.
Just out of curiosity, have you ever had the bass professionally set up, or have you ever done it yourself? I ask because if you have volume differences between strings that are larger than they should be, then adjusting individual string height would be the next step. Of course, if you go that way, you may as well get a full setup done to ensure proper intonation. I don't think you'll need to go that far, but if you've never done it before, now is a good time.
. It depends mostly on your budget vs time situation 
