I had the same issue when I took the Lakeshore Limited in 2007, but I got stopped in Rochester instead of Buffalo. Good for you for showing your college ID. I don't know if the rules have changed, but at the time, Amtrak's policy was that college IDs are sufficient for boarding. That was the argument I used with my ICE officer anyway. Also sadly, the color of your skin helps. I believe I was let go because the ICE officer couldn't wrap his head around the idea of an illegal Asian girl who spoke perfect English.
FWIW, I told my officer, "No I am not a US citizen" and proceeded to give him both my college id and (hesitantly) my visa-less passport.

I really don't know why Dreamers continue to take the Lakeshore Limited route- guys, seriously, please stop. There are other routes. It's been proven time and time again that the ICE agents make a stop on that train. My ICE officer said that they board trains that are within 120 miles of the border.