OK, first, lets make sure we have our language strait. When you say ammeter are you really talking about a voltmeter or multimeter? If you really are talking about an ammeter, then it sounds like you're connecting an ammeter from the output to, what, ground? If so, you're shorting the Pin3 output to ground.
This looks like a good YouTube video on how to use a multimeter and how to make various measurements: How to Use a Multimeter for Beginners - How to Measure Voltage, Resistance, Continuity and Amps - YouTube
So, make sure you are using a voltmeter or if it's a multimeter, then make sure you have it set to DC Volts. Then:
First I would check the voltage at the 3V3 pin. It should not vary. If it periodically (i.e. once every 2 seconds), drops, and then a second later, rises back up (for example, is 3.3 for a second, then falls to something like 1.8 for a second, then pops back up to 3.3), then the motor is placing too great a current demand on the Arduino's internal regulator -- which is what I'm fairly certain is going on here.
Second, if the 3.3V line is not fluctuating (radically), then perhaps your motor can't run at 3.3V -- you said that the "Motor works", but it wasn't clear, to me, exactly how you made that determination (I wasn't sure if when you said "...and tried both 9v and USB power", if you were connecting that power to the Arduino, then powering the motor directly off the 3V3 pin, OR if you were connecting these voltage sources directly across the motor. Do you know what this motor is rated at: voltage wise and current wise?
According to the Arduino website, Arduino Uno 3V3 pin can supply up to 50mA, but that's probably a conservative value. The datasheet for the LP2985-33DBVR sets the max current at 150mA, but that's at the minimum dropout voltage, so it might be less, depending on how much heat is generated by dropping 5V to 3.3V. It has internal current limiting, and thermal shutdown, so that is what will determine how much current you can get out of this thing. And, in fact, the datasheet has a "Peak Output Current" rating of 350mA -- but that may not last long (i.e. thermal shutdown will, likely, kick in -- a temporary condition that will clear once the regulator cools down enough).
Also, when driving a motor, there is "start-up" current to contend with. That's the amount of current needed to overcome static friction and inertia. That current is a bit more than the current it typically draws when spinning or driving something mechanical. If the supply, or driver transistor, can't contend with this start-up current, you're either gonna get nothing happening, or "magic smoke" ;D
This looks like a good YouTube video on how to drive a motor using an Arduino Uno. A MOSFET is featured in this video, but the concepts are similar enough to make it of value. Notice how the motor is powered directly off a 9V battery, and NOT the Arduino supply. The transistor, used to drive the motor, basically, switches power to the motor, directly from the battery. The Arduino is what "flips" the switch: Arduino DC Motor Control Tutorial - YouTube