How can I convert a flow sensor's pwm output to logic level relay control?
There is a couple of ways that you can tackle this project.

1) Filter (integrate) the PWM signal into an analog level that you then compare against a reference voltage.  This is probably the easiest method but it may not be as accurate as other methods.

2) measure the PWM duty-cycle with a microcontroller such as a PIC or Arduino board.  This requires software but has the advantage that it can be more accurate than the first method.

Question 1: does your sensor have an open-collector output?

Question 2: what is the PWM frequency?  What duty-cycle range does it provide?

Question 3: are you certain that the output is PWM with variable duty-cycle as opposed to just variable frequency?  Many flow sensors use a rotary vane with sensor and their output signal is a pulse train who's frequency varies with flow rate.  This requires somewhat different measurement techniques than what I described above.