I took the train from NYP to Montreal back in summer of '02, and it was a terrible ride. The train was delayed about 5 hours on the way up and 2 hours on the way back. Customs was actually pretty efficent, the only hold up was on the way back. Someone didn't have the proper paperwork and had to be taken off the train, and they weren't too happy about it. The two redeeming qualities about it were the price, much much cheaper than flying. Secondly I called and complained when I got back, and they gave me a certificate for the full amount of the tickets.

If price is a factor and you have the time, then the train is the way to go.