clock doesn't start

[Troward]

NFHS:
Visting team A leads by one point and has the ball for a throw in at half court with 5 seconds left in the game. Team A sends everyone towards the basket they are shooting at except for one player, A1, who cuts into the back court. B1 is defending A1 and gambles for the steal but his momentum takes him way out of the play. A1 catches the pass and there is now no one anywhere near him. A1 is just holding the ball and is easily going to run out the clock. I had watched B1 fly by to ensure there was no foul and then I glanced at A1 to make sure he had caught the ball cleanly, maybe 2 seconds have passed. Then I glance at the clock which to my dismay has not started.
If I whistle the ball dead I am penalizing the visiting team who has the game in hand by making them inbound again with 2-3 seconds to play. Can I whistle the play dead and declare the game is over without the clock having started? Should I hold my whistle and count off the remaining 3 seconds in my head and then whistle? If the clock suddenly starts (late) and I am the only one who saw it not start on time and I have whistled before the horn that could get ugly...
What would you do?