I was wondering what types of particulate matter is estimated by HOMER? I imagine it is PM2.5, but I do not see that specified anywhere.

You can define the particulate matter as PM2.5 if you want to.  HOMER is not concerned with the size of the particles or how deeply they enter into your lungs.  It simply multiplies the generator's fuel consumption (or the grid power purchases) by the emissions factor you specify to calculate the emissions of that pollutant.  The quantity of emissions will affect the net present cost if you specify a cost penalty for that pollutant, and it will affect feasibility if you specify a constraint on the emissions of that pollutant.