The amount of sugar in the fruit can be measured with a Brix meter. A drop of fruit juice is put on the glass and through the light refraction you can see how much % sugar the moisture contains.

However, I can imagine that the juice around the seeds has a different sugar content than the juice from the firm pulp.

What is the scientific way to get the right juice from the tomato fruit for a correct Brix measurement?

Well i would assume that blending several hole tomatoes together into a juicer would give the most accurate AVERAGE brix

Blending makes sense to get an overall value for the fruit.
I think the important thing is to establish your procedure and follow the same method every time, whichever way you prefer to take the drop.
You could try taking measurements from different parts and see if the difference is significant or not.
Another thing you could do is to use a tomato with "known" brix and use it as a standard to compare others. I have seen some values reported somewhere, Sungold for example. Not sure how much that would vary in different growing conditions.
And of course, you could find some publication which describes the method already used, and follow that if you think it's suitable.

Here's an example:
https://www.tandfonline.com/doi/pdf/10. ... 98.9514052
"Tests for °Brix, total solids, titratable acidity, and pH were performed on fruit homogenate, sometimes termed puree, single-strength juice or pulp, which was formed by blending the heated samples in a food processor for 40 s. "
Heating is required for viscosity test, but not necessary for Brix measurement. Since water has to be replaced it would be simpler to just blend your samples without heating.
"Fruit quality analyses followed the standard analytical procedures used in the laboratory of Heinz-Wattie Foods in Hastings, from the Official Methods of Analysis manual (AOAC 1970). This involved heating fruit by microwave oven to 94°C, termed the"hot break" method, to stop enzyme activity and separation of serum from solids. This is required for measurement of viscosity in fruit homogenate (puree). Evaporated water was replaced and samples cooled to 20°C for analysis."

I also think that the sugar content at one end of the tomato is greater than the other. I forgot which is which, but it's true for most fruits.