One approach could be to identify factors of sustainability and corresponding metrics that could be converted into an indicator to differentiate between the two fuels? Alternatively, any of the existing indicators of sustainability could be used to compare the two fuels.

1. Replacement / cannibalization of land used for food cultivation.

2. Natural resources used during whole life cycle.

3. Environmental impact.

4. Other factors. 

Answering this question is not straightforward and very complicated. Someone can answer if knows exactly the raw materials and other environmental and economic aspects of their supply systems. i tend to believe that ethanol form lignocellulosic residuals is , in general, sustainable. 

I think that the attached can help you.

Article Biofuels: A Survey on Pros and Cons

One of the problems with bio-fuels is that people desperately want to make something that mimics diesel, petrol, kerosine...so that they can use the same infrastructure and carry on with their lives. The whole idea of Drop-in fuels is inspired by this. Butanol is indeed an interesting fuel, but when you make butanol instead of ethanol, the yield will be much lower, just count the carbons and you know one reason, another is that butanol is even more toxic to living cells compared to ethanol and the technology to efficiently convert feedstocks to butanol doesn't exist yet. In contrast, we have 5 millenia of brewing experience on Earth yielding some extremely alcohol-tolerant yeast strains. We are capable of making bio-ethanol, it is easy and extremely efficient, we just have to use the right crops for that. When we drop the idea of being lazy and pretend we can't change existing infrastructure, then we only have to consider 1) the yield of fixed carbon per surface and time and 2) the quality of the resulting feedstock (how easy is it to turn it into a useful bio-fuel), and 3) long term sustainability and flexibility (is it an annual crop, can it be rotated with other crops, and what else can you do with the crop besides making bio-fuel.

To answer the specific question in the header, definitely bio-ethanol! Sugar crops and starch crops are far more productive than oil crops per surface and per time of cultivation. For instance, 20 tons of pure starch from potato per hectar in just 6 months growth is easily achieved. Typical oilcrops (oilseed, sunflower) are hard pressed to yield just 1 ton of oil in a year, only oil-palm can get to 3 tons, but even then that oil is more valuable as food than fuel. 

Change to new infrastructure will come gradually, existing machinery will stay as it is, but as bio-ethanol will be come available cheaper than hydrating it from ethylene (distilled during fossil fuel fractionation), people will invent appliances that run on ethanol. And think of this: if you have a tank with diesel in your garden and it leaks, your garden becomes special waste for the next 25 years. If it is ethanol, it will be bio-degraded within days. A large oil-tanker sinking in the seas leads to an ecological disaster, if it has loaded ethanol, it will simply mix with water and the microbes will decompose it within a few days. And ethanol burns with a beatiful blue flame, no smoke, no pollution.

The answer is bio-ethanol!

Bioethanol

It really depends on your source. Biodiesel got a bad reputation because in the rush to produce it, virgin oils were used which competed with food, but you can also use non-edible oils or, even, better waste cooking oils. Similarly for bioethanol, you can use sugar cane and compete directly with a food source, or use sugary wastes, such as fruit pomace for fermentation.

The other thing to remember about bioethanol is that there's a potentially larger market for it as ethanol is also used as a solvent and reagent in the chemical industry. Biodiesel has much less competition.

Both have pros and cons in terms of their fuel properties, so it's horses for courses in come ways, but by producing them from waste sources rather than virgin ones, both can be made more sustainable.

 Bioethanol is sustainable not only in terms of its present use as a fuel sources but also with respect to the future technology available to meet energy demands. For example Fuel cell technology and hydrogen are the best sustainable option to meet energy demands, Transportation etc in near future and their ethanol still exist as a best sustainable option. Ethanol steam reforming for hydrogen generation, Ethanol fuel cell....etc. 

Evaluating the economics of biofuels using full life-cycle accounting for biodiesel from soybeans and ethanol from corn grain, biodiesel yields 93% more energy than the energy invested in its production, while ethanol yields only 25% more.

This advantage of biodiesel over ethanol comes from lower agricultural input and more efficient conversion of feedstocks to fuel. Hence, compared with ethanol, biodiesel releases just 1.0%, 8.3%, and 13% as much agricultural nitrogen, phosphorus, and pesticide pollutant, respectively, per net energy gain.

Biodiesel also releases less air pollutant per net energy gain than does ethanol. Thus, relative to the fossil fuels they displace, greenhouse gas emissions are reduced 41% by the production and combustion of biodiesel, compared with 12% for ethanol.

Bioethanol is more sustainable compare to biodiesel in the respect of natural resources.In the production of Biodiesel by the process of transesterification,we can use methanol a non renewable alternative fuel,but if we use bio-ethnol a renewable alternative fuel to substitute the petrol where as biodiesel is also a renewable energy resource substitute the Diesel.Although both diesel and Petrol are non-renewable fossile based fuel.So bio-ethanol itself a alternative substitute fuel  of Petrol E5,E10--. It  may be used in place of methanol for the production of Biodiesel in the process of transesterification.Bioethanol is also a plant based fuel ( Baggass-cane sugar), so it is more sustanable inn comparision to others.

Both are same

Sustinability is depend on the availablity of rawmaterials. However, bioethanol and biodiesel both are sustinable. But, biodiesel canot produced only presence of bio-based product of oil. It requires methanol and a catalyst which mainly comes from chemical process. Even the bio catalyst could be employed, methanol should have to synthesis chemically. Methanol can be reply by ethanol which is bio-based product. Hope you get the full answer.

both. It is depend on the raw material you use for production of the biodiesel and bioethanol.

Dear A. Hajighasem ,

Bioethanol is more sustainable due to its ecofriendly production, availability, less environmental pollution compared to biodiesel extraction and also Biodiesel provides alternative solutions for future energy demands in countries like Sri Lanka where scarcity is abundant in terms of crude petroleum .