Can I put Li-ion batteries in series and discharge them at different voltages?
Would it be wiser to just use two buck converters from 14.4V down to 12V and 3.3V respectively?

Yes, that would be a MUCH better idea. Tapping off 3.6 V for making 3.3 V is a BAD idea as you would be using that single cell differently (loading it more) compared to the other cells. Then this cell's charge state will at some point be different from the other cells.

Also if you charge the cells the other cells could be fully charged while that single cell isn't fully charged yet. You would need separate charging circuits to handle this properly.

Also that single cell will wear out sooner than the other cells.

Using a buck converter to make 3.3 V from the 14.4 V is easy and much better design wise as all cells will be treated equally.