"Percentage of ... Higher than that [of/in] ..."

Starting with

The percentage of tiny devices in the IPs dataset is higher than that of the top websites.

If you add one word

The percentage of tiny devices reported in the IPs dataset is higher than that of the top websites.

and follow it through

The percentage of tiny devices reported in the IPs dataset is higher than that reported of the top websites.

It becomes clear that "of" is wrong, so using the same preposition:

The percentage of tiny devices in the IPs dataset is higher than that in the top websites.

Both are grammatically correct but have different meanings. "of" implies that the dataset was from the top websites themselves. "in" implies that the dataset is part of the top websites. a good example of the difference here would be

They are of Canada

They were born in Canada, but it is implied that they are no longer in Canada

They are in Canada

They are currently within Canada, but it is not implied that they were born in Canada