If it is not a bass set-up problem such as sound post adjustment, brand of strings,etc., or a built-in weakness of sound on certain notes then perhaps check out the following -
(1) Bow contact point. The E string sounds weak and indistinct when bowed over the fingerboard (Sul Tasto), perhaps more so than the A and D strings (but avoid sul tasto on the G string!!). It also quickly becomes stiff and harsh sounding as you move the bow towards the bridge. Try around 1 - 2 inches below the fingerboard
(2) Check out the ways you are sitting and standing to ensure that you are maintaining a 90 degree angle to the E string as you bow for best sound. If the bass leans a long way towards you this may change both the contact point and angle of bow to strings as you cross from higher strings.
(3) As well as the contact point check out the bow speed and weight you are using when the sounds are weak. The heavy E string requires less speed and some more weight, and some more care with contact point. As each string becomes thinner it generally progressively needs a faster bow speed to support the faster vibrations. On all strings there can be a trade off between each of the three variables for tone and projection.
(4) Are your LH fingers not quite getting the string down firmly on the fingerboard? If your wrist is heavily pronated to play on the E string this can rob your fingers of strength so look at the way you stand and sit and try altering the angle of the bass to your body. Also compare the sound when you play A flat with first your pinkie then your 2nd finger
(5) Is the string clearance at the nut too high? It should not be much more than the thickness of a business card.
(6) Try varying bow hair tension a 1/4 turn at a time, up and down, to bend the hair around the strings and get the best sound and attack with your bow.
I will often not use more than the lower half of the bow (the "comfort zone") for E string notes unless they are longer. I stay away from the end of the fingerboard except for fast passages, take care with note starts and use a slower speed and more weight to ensure that the string starts quickly, moves strongly and generates a full sound. I have seen my colleagues use longer, faster bows that moved the strings widely and yet they have produced a weaker sound that lacked focus and projection. Visually I was at odds with them and had some trouble with conductors who wanted us to lash at the bottom notes with fast full bows.
For tone and weight of sound try going back to basics. With contact point about 2" below the fingerboard and using firm but not heavy weight gradually slow the bow speed down until you can feel the weight of the vibrating E string resist the bow movement. You should see and feel the string move widely and produce a heavy warm sound for very little input from you. The bow hair bending over the string feels hooked onto the sound and as you speed up and slow down, plus or minus a bit of weight, the string should go with you. Avoid bow skid (too fast and light) or crushed sounds (too slow and heavy). I liken it to a surf board propelling the wave rather than being propelled.
Lots of fun experimenting?
Cheers, DP