Q:

Getting from Toronto to New York

I'm looking for a cheap and comfortable way to get from Toronto to New York.
By cheap I'm referring to anything below 100 USD.
Comfortable means, that I want to have a regular seat on a public or private transport vehicle. It shouldn't last longer than 12 hours. And if possible the border processing should be as fast as possible. I would be fine with flying, train, bus, private cars, ships, etc. The transport opportunity should be available for 2 persons around the first week of September.

A:

Amtrak runs daily trains for $114 that takes 13 1/2 hours, both of which are just above your thresholds.
Greyhound offers overnight buses that fit your requirements (10 1/2 hrs, $40 if buying now), or daily buses that take longer (presumably traffic related) - 12 to 12 1/2 hours.
Overall I'd recommend the bus, unless someone can find a plane flight for cheaper (I couldn't).  If you can make your own way to Buffalo there's $65 flights from there to NY via JetBlue and other airlines.

A:

Porter Airlines
I flew this airline last week between YTZ (Toronto Island Airport, a.k.a. Billy Bishop Airport, in downtown Toronto - note this is different than Pearson International, a.k.a. YYZ) and EWR (Newark).
The total roundtrip cost was $249, which included one-way fares of $69 - it was on sale, so it may not be available at the time you book, but they have sales often.  The taxes and surcharges broke down as follows: $42 in charges and taxes on the Canadian side (including the $20 airport improvement fee), $58 in six different charges and taxes on the US side (including the agriculture tax), and $11 in sales taxes.
Not exactly $100 one-way, but it's an option to consider as it takes significantly less time than train or Greyhound.
Porter doesn't pay to play, so you won't find it on major travel search sites.  What I like about them is that they provide very good service and have done a good job eliminating the annoying waits and delays at airports.  Alcohol and 34-inch legroom on board.  You can arrive 30 minutes before the departure and be on your way into town 10 minutes after the arrival.  This airline is our best-kept local secret and many people choose it for short hops to Ottawa, Montreal, Boston, New York and Northern Virginia.

