A guess: Current peaks of LM2664 Charge Pump DC/DC converter go through your signal GND wiring and cause noise voltage due the resistance and inductance of GND wiring.
If you look at the datasheet of LM2664, you see that there are three capacitors connected directly to LM2664. No tapping is allowed to other circuitry between the capacitors and LM2664. In addition the wires between your main power supply and LM2664 shouldn't be any part of signal wiring. Most impostant this is for GND.
These requirements are the same as in all device designs which contain analog circuits and logic or pulse circuits. No pulse or logic circuit currents are allowed in analog signal GND wiring.
ADD: Oscilloscope measurements can also generate noise if there's long ground connections for the scope or mains power wiring creates ground loops. You should test does your measurement catch additional noise (have a high frequency signal transformer + DC blockinc capacitor in the input of the scope or feed your circuit with DC from a battery) USB refers you have a computer. How many separate ground connections you have via the computer? One GND connection only is allowed.