If by "on" you mean "in" the station, then No. Any bag left unattended inside the main station will be confiscated by police for fear that it may contain a bomb or other harmful agent. That assumes that it's not stolen first by some thief.
If you are lucky enough to be able to gain access to the Club Acela lounge, then you can leave your bags there for free. But you either need to be traveling in First Class or Sleeper Class on that day, or have one of the passes sold for AGR points on the AGR website. Of course if you have Select Plus status, then you also have access to the lounge.
Otherwise your only alternative is paying to day check your bags at the Amtrak baggage counter, or taking your bags with you.