2) is correct. We use "at [somebody's] disposal" as a modifier for a person or thing [noun/noun phrase]. For example: "Napoleon had a huge number of soldiers at his disposal" "I'll leave my car at your disposal this weekend" "If you ever need help, I am at your disposal" 1) is not correct because we use "[verb] at will". For example: "Ronaldo is so talented, he seems to score at will" "Fire at will" 3) is not correct because we use "at [somebody's] discretion" as a modifier for an action or event [noun/noun phrase/gerund] that depends on [somebody's] decision, not for a thing (like funds). For example: "Service is at the company's discretion and may be terminated without notice" "We do not offer insurance. Any risk is at the customer's own discretion." "I leave it at your discretion whether we speak again this week"

I would use sentence 2. A native speaker probably wouln't say 1 or 3.

2 = most naturally correct. 3= good you can say that it means the same thing in essence. it is only a linguistic or grammatical difference, but you are conveying the same underlying message. 1 can be altered to say the same in a different style of speaking. 1. We can use our enormous funds at will on this project. 2. We have a lot of funds at our disposal to use on this project. 3. We have a lot of funds at our discretion to use on this project.