usually its the same amount of time. The only priviledge Non-profit organizations have over For-profit companies is that they can apply for H1B at any time of the year and there is no limit.  while For-profit companies can apply for H1B only from 1st April and the emplopyee can start working from October 1.  Usually it takes around 3 months to get H1B approved for regular processing and only 15 days for  premium processing until and unless the DHS sends you RFE (Request for Evidence) which may lead into double that time period.

My company (Non-profit org.) filed a premium processing for me and they sent RFE exactly on 14th day and after receiving the proof they took another 13 days.   For premium processing they have to decide within 15 days time-frame but there is no time limit for regular processing so they may take 1 month or 5 months. so you are better off if your company does a premium processing. good luck