I'm a big Spycraft player, but then again, I'm biased, being on the Design Team and all.
Actually, I own and play both systems. I like d20 Modern and all, but it IS very "Buffy" while Spycraft is very "Bond." Flavor is the whole thing.
I also use Spycraft for anything action-oriented, not just espionage. For example, I've run the Matrix using Spycraft, as well as a game set in the Metal Gear Solid universe.
I highly reccommend the d20 Modern book as well; incredibly well put together, nice artwork, and a lot of generic options. Still, for the kind of game you're looking at, I'd go Spycraft all the way. Don't worry about a lack of support; the support from AEG is going to continue to come in droves, and there's a pretty large fan base.