Is it better to PWM the output of the boost circuit before the LED strip with some sort of FET, or to PWM the enable signal to the switching regulator itself?
If your boost circuit does have an enable pin that's fast enough for your job (most have, some don't), use that. It saves you additional circuitry, at the very least, and you'll never run your boost circuit without load (which, again, most modern switchers could withstand, but not knowing yours, I can't tell).
Also, if you're concerned about efficiency, start by eliminating the series resistor on your LEDs! That's where energy is wasted. Since you already have a reliable power source, you should be able to run the LEDs directly if you just reduce the output voltage of your boost converter accordingly. In fact, for LED applications, there's even current-controlled boost converters, so that you build a constant current source instead of a constant voltage source – exactly what your LEDs need.