I suspect that you may be misremembering the lyrics slightly, but that's pretty common. I searched multiple lyrics databases and did not find a song that precisely matched what you recall. I think I know what song you're thinking of, however. "Holes in the Floor of Heaven" by Steve Wariner (1998) describes a deceased loved one whose tears from heaven pour down, and the loved one watches from above. Here are the similar sounding lyrics:
There are holes in the floor of Heaven
And she's watching over you and me.
There are two reasons I believe this is the correct song: 1) its lyrics are remarkably similar and 2) the lyrics you recall about heaven having eyes doesn't quite make sense.