Given the restrictions that you described, I would be inclined to decide if an alternate route for the pipe is available if the garage should be built and the pipe should fail at some point thereafter. Will adequate access to the well itself be available?
If the answers are yes, I would just not mention the pipe at all-- and build the garage. It is unlikely that any official record exists of the location of the pipe and even if it does, it is unlikely that any official will bother to look for it.

Murphy WILL strike. Reroute the pipe before building the garage. Or, you may have some weeks of downtime during a blizzard or 100 degree heat while that gets done. All with you not having water during that time. Better to address the new route while the old one is still serviceable in place. That way, you're only without water for the small time it takes to switch it over to the new line.