Outboard A/D converters are always to be preferred to onboard converters when good clean results are needed. But aside from that it takes extra extra care to make onboard converters behave properly.

There has been some general discussion on this subject on the forum here. Grounding, routing, power distribution and filtering are very critical but I suspect one of the most effective strategies to your problem is to put the processor into sleep mode while the A/D menasurement is being taken.

Michael Karas