Not much is known as of yet regarding the crashing of an MQ-9 Reaper into Lake Ontario, New York around 1 PM on November 12, 2013. No information has been released other than the Remotely Piloted Aircraft was being flown as a tool for Air Guard’s Syracuse-based 174th Attack Wing to train Air Force pilots on how to use the MQ-9.
It is likely that the vehicle crashed into the water and that crews have yet to locate the vehicle. We can assume that the vehicle lost connection and went to a controlled re-establish pattern as designated by the pre-flight computer checklist in order to prevent total loss on the ground and to protect local communities.
We know from an AP report that the vehicle was unarmed and there is no concern as to armaments in the lake or elsewhere. As more information becomes available, it will be released. 
From this point on there will likely be an accident investigation by the FAA into how exactly the aircraft was lost – whether a lost link connection is to blame or if a chain events unfolded which led to incorrect decision processing or situational awareness becoming compromised. The MQ-9 control systems are known for the inadequate human factors design and extensive fatigue driving control mechanisms; many pilots finding the control scheme to be much more “unwieldy” and “unnavigable” compared to a standard fighter jet.
SOURCE: http://abcnews.go.com/US/wireStory/ny-military-reaper-drone-crashes-lake-ontario-20868618