I was afraid of getting excessive noise as well when I took the rubber feet off of the pump and there is a low-level hum to it that honestly doesn't bother me. It sounds like a lot of other pieces of electronic equipment in my house, but I am not sensitive to noise either. I also make sure that the pump is completely flat after I service it (no side is slightly higher than another).Like to ask, are you getting vibration noise from the eheim since the base is off?
I had read that if you do have vibration noise, you could cut out a piece of cushiony rubber that you can place in the bottom of the chamber and then sit the pump on top of it to dampen the noise. Not sure how well the rubber would hold up in saltwater, but the idea sounds logical and you can use whatever material will work for you. I would have tried that method if the pump noise drove me crazy. Hope that's helpful.
PS - If I manage to figure out how to insert a video, I'll post the one I took to show the pump noise.