How long are your pulse widths? If they are in 10's of msecs, then you could probably get away with software timed loops to produce the PWM signal from a digital output.
If you require shorter pulse widths than that, you can build a pretty simple PWM circuit that uses 3 op-amps to produce a square wave based on a voltage reference. I.e., 0V input for 0% Duty Cycle, 5V input for 50% Duty Cycle, 10V input for 100% Duty Cycle. Then you would use the analog output from your USB-6009 board to set the duty cycle. The timing of the square-wave could be set by an RC time constant. Just an idea... you wouldn't be able to change duty cycle % very quickly, however. Again in the 10's of msecs I would imagine. But it would give you shorter pulse widths.
Basically, we need more information about what you are doing as the hardware you have choosen to do the task makes the job non-trivial.
