There's a church just down south of Sanctuary.
Usually churches also have second floor where they have boxes there.
And I don't think it's a good idea to keep your stuff outside settlement. lol.
Test out the boxes in concord.
Beside the main quest in that area there is a church but like I said test the boxes.
Don't wanna lose all your godly weapons
Now that I think of it you can google " fallout 4 map" and the first one is an interactive map that you can customize quickly to show only church locations.
However i just looked and the one I am talking about above is not shown. Interesting lol.
Outside of the settlements, no storage is safe. Exception are workbenches (armor, weapon and power armor). I have newer lost items in one, including those outside of the settlements.
I suggest you build your own church inside one of your settlements.
Don't forget to build a pit to put a burning sacrificial settler. LOLZ
The Old North Church (above the Railroad HQ ). Enemies never respawn inside of it. It`s quite ruined and dirty though and there are only 2 containers: a suitcase and a cooler. Nothing spawns inside of them since I looted them in the beginning of game. I never tried to put anything inside, so I don`t know if they are safe . But the good thing about the place is that you can use Railroad HQ , there are many workbenches there.
I also remember there was a Church not far from Murkwater construction site and there is a Church in Cambridge, not far from the Police station. But I don`t know if they can be used to keep your stuff there.
There's a nice church north of federal ration stockpile. I don't have the map in front of me but I believe its south westish of Walden Pond, south of the freeway and the stoner robot location.
There are some beautiful churches in Boston, but I'm not sure if you can go in them.