A windmill would have the lowest operating cost - energy is free and you have small annual (or less frequent) maintenance costs. The last time I compared setup costs, they were roughly a wash (maybe $200-$300 difference depending on whether you were comparing deluxe apples to average oranges or vice versa). The aeration Pros can give much more exact quotes on prices as well specs such as air delivery, etc.
I have a windmill. I like the no-electric-bill part and I enjoy having the windmill spin around at the pond instead of hearing compressor noises.
BUT (and it's a big but), you can do a whole lot more with electric aeration than you can with a windmill. You're not dependant on the wind blowing, which might not happen when you're under a fish-kill threat in mid-Summer after a dense algae bloom dies and you really need the extra oxygen in the water. You don't need to pay for electric to run it 24/7, because you won't need it all the time (some months probably not at all). I think most compressors are capable of driving more than one airstone/diffuser, and most (or all) windmils aren't. And you don't have to bury a long electric line to take power to the pond, you can put the compressor (and the noise) at the nearest electric source and bury the airline - some of us consider that safer than and/or preferrable to buried electric.
I think if you are planning to intensely push to envelope in your pond (fertilizing, heavy feeding, highest possible weight of fish) you are much better off with the capabilities and capacity of electric aeration. If you plan a more laissez-faire approach, a windmill will probably prove sufficient.
Right now, I am happy and believe I am well-served by my windmill. But if/when I retire, put in a second pond, and push the envelope, I should probably put an electric compressor in my nearest barn and run airlines to both ponds. The windmil will probably need replaced by then anyway.