ZBW controller described a potential conlfict event when the flight plan status; IFR or VFR; was uncertain; the reporter claiming the automation between N90 and ZBW needs to be fixed to reduce these types of situations.

Narrative

My RADAR Associate took a manual hand off from N90 Catskill Controller on Aircraft X. He told me the aircraft was VFR to PTK. I started the track and put in a VFR flight plan. Aircraft X checked on frequency climbing. I verified the type and destination; as my D Side was not sure of the information he just took. I had traffic landing SWF opposite direction descending to 110. At that time Aircraft X's altitude indicated VFR/100. I asked Aircraft X what altitude he was climbing to; so I could determine if I would need to vector one or both of the aircraft; or just call traffic. Aircraft X responded that he was level at 100. I asked him if he was VFR or IFR. He stated that he was IFR. I then cleared him to PTK via direct and maintain 100. I then asked him if he got the IFR clearance from New York. He replied; 'No I did not; I mean yes I got the clearance from New York'. My D side then called N90 and asked them what kind of clearance Aircraft X had; IFR or VFR? N90 (from what I could hear my D side say; and what he told me) said that he was VFR. Recommendation; the automation between N90 and ZBW needs to be fixed. It is very difficult to initiate/accept hand offs to/from N90 on aircraft that get airborne clearances. It seems that if the aircraft has filed a flight plan in the NAS; the automation will work; but once airborne it is very difficult. If the automation between N90 and ZBW was fixed this would not happen; as a flight data block would indicate the type of flight plan the aircraft is on.