This is actually a lot tougher choice than it first seems, as you tend to pick out certain tracks, but then consistancy comes into it...
For example, Skull Fang by Data East has probably got one of the best soundtracks of any game I've ever played, but Im pretty hard pushed to actually think of any other game they've done that is in the least bit memorable (apart from maybe Vapor Trail, which is skull fangs prequel) so in my view it'd be unfair to vote for them off the back of 1 game.
The nod for me probably has to go to Sega, for pure consistancy and quality, only marginally nosing ahead of Konami, with Taito coming close behind, its pretty much hard for me to choose between the 3 of them as they each have outstanding contributions to the whole genre, but I feel that Sega has probably had more influence
than any of the others.
Konami are, musically, arguably better, but their approach seems to be refinement/evolution rather than revolution, and shamelessly heavily plagiarising themselves and others to great effect
So, there you go, what do you think!