It could be that the lift pump did in fact fail at that exact moment however it probably (hopefully) isn't the case. Once the siphon is broken a fair amount of air will enter the system but remember that your raw water inlet and the lift pump are usually below the boat's waterline. (depending on boat model, etc.) so now you just have a bucket of fluid with no pressure to reprime the pump.
How long did you let your engine run before shutting it down? When is the last time you replaced or inspected your raw water pump? Supplying the fluid to the engine under a standing fluid column (gravity feed) should reprime the pump.
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