The directions that come with your tension gauge tell you to
test with the thread through the eye of the needle.  I do know
that lower, and more accurate readings will be obtained with
the thread NOT going thru the eye.  Needle eyes can have
different sizes and even shape, dependant upon the size,
brand, (style such as ball point vs semi-ballpoint-vs sharp) and
finish of the needle. Also, the angle and direction you pull at
thru a threaded needle can be very critical, which can result in
problems getting repeatable readings, especially on some types,
brands, and colors of thread.

It is more important to get the bobbin tension set correctly, since
you are really only setting the top tensions up "in the ballpark",
and you have done an "H" or "O" test design to make sure 1/3 of the
thread on the back is bobbin thread.