Just wondering if anyone has flown JFK to Boston lately?

I've a direct flight Bangkok to JFK, but haven't sorted out the JFK to Boston bit. Tried to through a travel agent in Laos, but they were going to charge a simply obscene amount. From what I can gather the commuter flights are pretty cheap, but can they handle a bike as luggage?

Part B: I was hoping to not box my bike. I haven't had to yet this trip, including 4 overseas flights so far.

Any info would be very helpfull. Likely will not have internet access for a few days, untill Hoi An.

Thanks, and cheers from Hue` Vietnam!