I've seen 5000 watt diesel generators new selling for $999, and 5000 watt 'whisper quiet' diesels selling new for $1600. And being new equipment, they should be ready to run bio-diesel as-is.
The down-side, aside from the high cost, is the weight. Most generators I've seen in that range weight between 200-400lbs. If I had the space, the ability to move it easily, and the money, I'd be all over a diesel generator.