Gautam, buses are very frequent from the Port Authority in NYC and are no problem. Round trip will cost you between $70 (Bonanza) up to $130 (Coach, Peter Pan, Greyhound and those). Or you can take Amtrak or Acela (the fast train), which is prolly more comfortable and more expensive (Acela around $200). Bus and train take around 4 1/2 hours, Acela around 3 1/2. There are frequent flights to Chicago, best carrier seems to be ATA (I was just booking flights to Chicago yesterday) and if you are a bit flexible with time of the flight you can get a ticket for about $200 to $230, but even if you need exact times it should be under 300.
There are plenty of good places to stay in Boston - especially around Harvard Square in Cambridge there are multiple nice bed and breakfasts and inns - like Inn at Harvard, or Kirkland St. Inn. If you check out
www.bostonphoenix.com, there is a lot of links and such. You are welcome to stay with us, if you'd settle for an air mattress. Comes with royal breakfast, provided there is food in the fridge!
Soooo excited, I already marked the calendar. Tell us what you want to see/do, so that we can prepare your itinerary for Boston!