The missing numbers could be 9 and -9:
3,9,3,-3,-9,-3.
The pattern is, starting at 3, up 6 units to 9, down 6 units to 3, down 6 units to -3, down 6 units to -9, up 6 units to -3. This forms a type of repeating triangle wave pattern as shown below, where the terms 1-6 are shown as points on the wave:
The horizontal green and purple lines enclose the maximum peaks and troughs of the wave, and the vertical orange lines represent by intersection where the terms of the series fit the wave.