I haven't decided yet. I am going to mock up the BeePre rebuild using plywood to play around with layout to eliminate/minimize noise. I'll test various options then. Battery is obviously the safest bet noise-wise, since the power supply wouldn't be connected to either the amp wiring or mains. But some folks on DiyAudio who've used fans report no injection of noise running the fans off the amp filament supply. B/c I'm installing separate filament supply transformers, the existing 6.3V secondaries can be repurposed - so I'll try running the fans off of those (after doubling/rectifying and smoothing) and compare with battery power. If I can't hear or measure any additional noise, I'll go with using the 6.3V windings. But if that proves noisy, I'll try a separate trafo (10 or 12V). I might even try (being the crazy guy that I am) using a C4S in from of them to isolate them - but this assumes that isolation of the C4S (which I assume is function of impedance to AC - but don;t know) works both ways: PS and load each isolated from each other. Not sure if it does work that way or is instead one-directional.
I think I may also install a pot to control dc voltage/fan speed. To be even fancier, one can install a temp sensor or thermistor that controls fan speed. I'm thinking about that, but will probably leave it as something fun to play with in the future.
cheers, Derek