Business class is really a judgement call. I personally feel like with the extra legroom, electrical outlets at every seat, non-alcoholic beverages, etc. make it a worthwhile investment (not sure about the beverages on the Regional trains you'll be riding).
New York for transferring is, well, interesting. I somehow manage to always exit through the wrong stairwell, don't ask me how I manage to do it. I believe when you arrive you will want to walk towards the rear of your train to be put in to the Amtrak waiting area, Alan please correct me if I'm wrong. 90 minutes is more than ample time to change trains. Just keep your eyes on the departure board and your ears open and you'll have no trouble. This would also be a good opportunity to grab a bite to eat if you feel it's necessary. You can access a large number of eateries by heading towards the LIRR concourse. To get there walk towards the high numbered tracks and just to the right of the Amtrak ticket windows there will be a small hallway. Walk through this hallway and you'll be on the LIRR concourse with a plethora of quick dining options, always a good opportunity to pick up a slice of New York's finest.
Finally,
here at On Track On Line they have a great set of tips for first time travelers like yourself that are very helpful. If you have any other questions feel free to ask! Have a fabulous trip! B)