If you want larger markers in a graph, right-click in the graph and select a marker size from the Marker Size menu. 
  Marker Size Menu
Marker Size Menu
  If you always want markers to be bigger in all your graphs, set the marker size in Preferences.
  - Select JMP > Preferences.
- Select the Graphs page.
- Select the size that you want from the Graph Marker size menu.
 Marker Size Preference
Marker Size Preference