Arduino Mega - 54 or 64 digital pins

The Mega MCU has four VCC/GND pins, which allow for 100mA each, so 400mA absolute max chip current. So you're ok with 2.27mA per pin.

Using 60 transistors could be a nightmare. Is this for your 12volt/3watt LEDs?
2.27mA seems too low for a 2N3904 to fully saturate with 250mA collector current.
Leo..