How do I track which Korok seeds are left?

Best of luck grabbing those last couple seeds, as you have no doubt noticed there are a lot of them.

I found that this interactive map is quite useful as you can filter it to show the location of all the seeds. Additionally when you click on the little seed icon, there is a small info window that pops up with a small photo and descriptor of that specific seed.

Additionally, in those little info windows there is the option to mark the seeds as completed/not completed. Then you can use the little gear in the top left corner to hide "completed" seeds, so you can track your progress as you go.

@Malco's answer is pretty good, and should be your method you use to find them and mark them off. However, I would like to add that if you have purchased the Master Trials DLC, there unlocks a quest to get a new piece of headgear called the Korok Mask. Check out this polygon article on how to unlock it.

From the article:

When worn, this mask acts like your sheiklah slate does for shrines, but for koroks.

Using Malco's method plus the mask should get you that totally awesome end reward in no time.

Spolier alert:

Its a golden piece of poop.