Why is my NPN base so slow to turn off?

The 3.3 V peak input voltage drives the transistor into saturation, which can take considerable time to recover from. Try using anti-saturation circuitry, such as a baker clamp, or lower the input voltage.

I had a similar problem, caused by driving the transistor into saturation as mentioned by Bart.

Because I already had the PCBs, adding a anti-saturation circuit would have been difficult. Instead I replaced the base resistor, originally 1 kohm, with 10 kohm resistor with 1 nF capacitor in parallel. The capacitor provides a current spike to rapidly change the base voltage.