Jet Airways, Air India, Indigo Flights available from Kolkata, as of May 2014.
As of now Manipur is not connected to other parts of India by train save for a small town of Jiribam. After you reach Guwahati in Assam by train you can go to the Network Travels which is walking distance from the railway station towards Manipuri Basti. You can book an overnight bus from Guwahati to Imphal they will take you in a shuttle bus from there to the state ISBT for about 700-800INR. Or you can choose for a longer journey by going round to Silchar through Shillong and take a SUV ride for 550INR from Jiribam to Imphal. The latter is more of an off-road drive and more fun for young and energetic people.