Hi Luis. I don’t know any good programs but beware of calculating a water footprint for milk, or any other animal product for that matter. For all of the examples I’ve seen the largest majority of water is used in the growing of the feed for the animals.
If you are in California or Mediterranean Europe then the source and cost of irrigation is a strong consideration. If you are in North East USA or Northern Europe, the water needed falls as rain so it is of less consequence.