I need a good motor controller to use PWM on a pair of 3 amp 12V bilge pumps. Will need to be designed for 24/7 operation potentially. Each motor has a peak of 3 amp so something that supports at least that on each motor, preferably more to be safe.
By "peak of 3 amp" do you mean the rated maximum continuous current draw?
If so, the startup/stall current will be between 15 and 30 amps. Make sure that your motor controller can easily handle the startup/stall current. Pololu has an excellent selection of motor controllers.
I just know the box says 3A and when I crank them up to 12V underwater thats about what each pulls.
To be safe, buy a controller than can handle at least 15 Amperes. The good ones will shut down to protect themselves from excessive current.