I prefer the sapling method simply because it's just easy to pipe the saplings into an enderchest that's connected to a Bio Reactor.
Right now, my biofuel production hands me about 4 buckets per minute WHILE running 2 HP boilers and a LP boiler. That could easily run another 4 boilers.
And the bottleneck is still my farm, though my bio reactor does occasionally get a little backed up. If I were to extend the size of the farm or add a fertilizer, the biofuel production would increase exponentially until it was bottlenecked by either the Bio Reactor, or the speed of my Harvesters.