Hi Martie,
You can set the comma separator by formatting the number for your field in the Fields View for the layer/table. See An overview of fields—Geodatabases | ArcGIS Desktop. The Table Frame will respect any number formatting you set. In the example below I've formatted the field "POP1990" to show the separators.

1. In the Contents pane right-click the layer or table you want to change
2. From the context hover over "Design" and click "Fields" from the pull-right menu to pen the Fields View
As you can see the Table Frame display the commas. I've also set the values in the table to be right-aligned.

1. In the Contents pane expand the Table Frame item
2. Right-click the field you want to change and click Properties to open the Format Table Frame Fields pane
3. In the Format Table Frame Fields pane click "Text Symbol"
4. Expand "Position" and click third Horizontal alignment option from the left
Hope this helps,
Tom