Since I've recently given this scenario some more thought, I thought I would expand on my post above. If a ZBW area B controller (CON 37 sector) happens to be lurking out there, your local knowledge would certainly be appreciated.
The radar coverage at LEB is poor or nil at best until at or above 4,500 - 5000 ft MSL so assuming the MVA is the same or higher than the MEA on V496, the controller would not be able to legally issue the clearance, "cross LEB at or above 3900, cleared ILS runway 18 approach." I don't have access to the MVA chart for that area off hand, but the validity of this clearance largely has to do with the MVA in the area (and if radar coverage is sufficient).
Now from a pilot's perspective, is there any way to know what the MVA is in a particular sector? Not really unless you somehow have access to the MVA charts which in flight is a slim chance. Some rely heavily on ATC to provide terrain and obstacle clearance though most of the time it is our responsibility. In this case, it would be rather difficult to know off hand that the clearance is or is not valid and thus whether complying with the clearance will provide adequate terrain clearance. Some quick pre-flight planning with a glance at the sectional chart and surrounding IAPs may lead you to question this clearance after you have some more information about the local terrain. If in doubt, it never hurts to ask.