Short answer: use the scheduler add-on: http://addons.heroku.com/scheduler
Long answer: When you do heroku run, we
- spin up a dyno
- put your code on it
- execute your command, wait for it to finish
- throw the dyno away
Any changes you made to crontab would be immediately thrown away. Everything is ephemeral, you cannot edit files on heroku, just push new code.