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You should apply for a Schengen visa via the country in which your longest stay will be, and if you plan to stay an equal time in multiple countries then you apply via the country which is your port of entry.
In your case, you should apply via the Netherlands.
Because I have a layover in Amsterdam, does that count as my port of entry?
If you fly from Amsterdam to another Schengen country, then yes that counts as your port of entry into the Schengen area. If you fly from Amsterdam via a non-Schengen country, it would not count as your port of entry into the Schengen area.