There's really no way to be the top bidder unless you offer a major league contract. If you're being beaten, I assume that either another team offered a major league deal, or there are other factors that are swaying the player toward the other team (I've heard that things like team success and quality of coaching staff are among the things that can lure a minor league FA).
Not that you asked for an editorial, but minor league FA's should generally only be used to pad out a minor league system that doesn't physically have enough players in it; to improve a "depleted" farm system (i.e. to reload with quality prospects) you'll definitely want to focus on IFA and the draft.