I had the problem of waking up with puffy eyes and face for many years. For me it tends to happen when my sodium is high and potassium low, particularly during the week before my period. I found that watching my sodium intake during this time, keeping hydrated and coffee enemas really helped. I have had issues with parasites and liver congestion, so I'm sure these are also contributing.
I found that muscle testing what supplements to take really helped. Often I needed extra B6, potassium or sometimes a multi vitamin (Megapan). Interestingly since switching to TEI supps I no longer get the puffy eyes, so there must be something in them that my body really needed.