What would be the choice... I have heard some nasty stuff about most everything but Vinegar....
I agree and that is why I choose vinegar. Perhaps I would not use the word nasty though.
The effect of a carbon source on bacteria is but one aspect of making a decision for what carbon source to use. Let's not forget about the effect on other organisms of interest like cyanobacteria, coral, the symbionts of coral, dinoflagellates and algae type pests.
I have found no research so far regarding the effect of ethanol on coral. Acetate seems to be utilized by coral and their symbionts. Is this good or bad. I have read no negative effects by hobbyists when dosing vinegar except when Randy found his limit for vinegar dosing which seemed to negatively effect his anemone. That was at a quite high dose of vinegar. On the other hand it seems from hobbyists posts that ethanol can adversely effect coral at much lower doses.
Hobbyists seem to report more problems with cyano from dosing vodka and the pellets. On the other hand vinegar does not seem to promote cyano growth by reports from many hobbyists. Scientific studies demonstrate that ethanol promotes cyano growth and acetate has no effect on their growth.
As far as the effect on bacteria, acetate seems to stimulate most bacterial types including aerobic and anaerobic which both are of benefit in a reef tank. At high enough levels acetate can have negative effects on anammox bacteria, but the level it takes of acetate is much higher than ethanol.
Ethanol seems to stimulate bacterial growth especially concerning the aerobic bacteria. At high levels ethanol can inhibit anammox bacteria, but not at levels that your typically dosed in a reef tank. Still this may be a concern depending on the volume that one doses ethanol in. If the ethanol is dosed in a smaller volume like a sump and then allowed to enter the tank, perhaps the levels in the sump may reach a high enough level to cause some problems. Vinegar (acetate) is much more forgiving in this respect. How ethanol actually effects the growth rate of annamox bacteria at lower levels is not clear to me from the research. It could increase the anammox growth rate at lower levels or perhaps have no effect at lower levels until the levels reach at point of inhibition.
As far as the effect that either have on other organisms I have found no research that helps.
FWIW, thanks to Randy's help by providing some calculations, research found that there was 70% anammox inhibition when ethanol was dosed at 87 ml of ethanol in a 100 gallon water volume. The effect of ethanol at lower levels was not a linear correlation and was considered specie Dependant.