So for some reason when I went to play Fallout 4 today all but one of my save points were gone, and the one I have is really old. I restarted playing several times yesterday and even on a different computers but my saves were still always there until today. If that data is floating around in the cloud somewhere or I could prevent this from happening in the future that would be great.

It might be a Steam Cloud issue.

Game saves are located at:

%userprofile%\Documents\My Games\Fallout4\Saves

edit: You could turn off the Steam Cloud integration, but save games would only be stored on your computer.

To disable Steam Cloud for Fallout 4. Right-click on the Fallout 4 entry in the Steam Library. Go to Properties, and then click the Updates tab, under Steam Cloud, uncheck the 'Enable Steam Cloud synchronization for Fallout 4' option. I wouldn't do this until the Cloud fixes itself as the saves will most likely be lost.