The reading values - above 3000 are very good, don't worry with this.
Try this: open the device (joystick ?) plug into computer USB port and careful move the magnets until the axis are centered (more approximately possible).
Instead monitor on Windows applet use one these joy test software, like this one in your above pictures, more detailed. The center is in 2048. The blue axis -static on second picture - is clearly off center.
The "Achilles hell" of DIY HALL sensor assembly is this alignment, a 0.1 mm off make difference in centering.
