Okay, you have the correct form for Ohm's Law, and have identified that you need to drop 6V across the resistor.
The problem you have, which you have also correctly identified, is the unknown current. Not only is it not specified, but it won't be constant either, changing as the load varies, the lubrication ages and even things like temperature. This is one reason why using a resistor to match your 9V supply to your 3V pump is not a wise choice.
The other reason is that using a resistor is horribly inefficient, and that matters when the pump is probably the biggest user of d.c. power in your system. Dropping 9V to 3V is 33% efficient, the 67% lost power being converted into heat, which you need to manage.
A better plan is to use a 9V pump, if you can find one, or use switch-mode-regulator to provide a constant 3V at a wide range of currents. To do this, you'll need to get a 3V pump and test it with a bench power supply and multimeter, under a variety of load conditions, to specify a regulator.
Does any of the above help?