Supplements are probably your best bet. The only way that leos get vitamin D from prey sources directly is by eating the liver of an animal that makes its own. Once a gecko starts getting the shakes, though, that means there isn't enough calcium circulating in the bloodstream to support normal muscle function so the odds are high they won't be able to digest a pinkie thoroughly and extract enough vitamin D. Plus rodents make a different form, vitamin D2 so there has to be enough muscle activity possible to convert the vitamin into the D3 form a reptile can actually use.
Calcium shots are the best way to get things headed in the right direction, with or without D3 depending on bloodwork results. Sometimes the animal has plenty of D in the bloodstream already and it's merely a calcium/magnesium/zinc problem.
Shaking can also be caused by a lack of B vitamins, dehydration, virus or low blood sugar. Seeing a vet and having bloodwork done is always best when you see the shakes so you make sure you are treating the right thing.
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