The main (level) viewport is always the accurate one when it comes to how an effect looks in your game. The Niagara preview viewport can have different lighting, geometry and a different tick rate.
A lot of the time, the difference comes from different fps in the viewports. You can check if that is the cause by going to the system properties of your effect and turn on “Fixed Tick Delta”, which is always a good idea to enable for effects that are very sensitive to fps changes (e.g. effects with a lot of velocity, constraints or radial forces).