NPN transistor is always on
This probably comes down to one of two problems:

You flipped some pins on the transistor.  If I remember right, on a TIP41 the left pin is the base, the center the collector, and the right the emitter.  This is when viewing with the black part of the package towards you and the pins down.  Of course don't take my word for this.  Check the datasheet.

The GPIO1 pin isn't actually changing state.  This is really easy to check.  Put a voltmeter between GPIo1 and ground.  It should be whatever the power supply voltage (usually 3.3 or 5 V) is when the LED is supposed to be on, and 0 V when its supposed to be off.

If the GPIO1 pin voltage is correct, then you almost certainly have the transistor wired up backwards, or it got blown out.  However, a TIP41 is not so easy to blow out, so probably wired wrong.

If the GPIO1 pin voltage is stuck at the power supply, then you have a software problem.



A good way to check your circuit is to disconnect R2 from GPIO1.  Then manually connect the left end of R2 to power and ground.  The LED should be lit when it's connected to power, and not lit when connected to ground.  If that's not the case, then the problem is with the transistor or how it's wired up.