I say the 390. Despite some opinions, FE engines have had a large resurgence in popularity over the past 3 - 4 years. There are several FE engine specialty businesses you can buy parts from, gain advice from or even purchase a 'crate' motor from.
So here's my question. If the 360 (which I have in my 75 F250 Highgboy 4X4) runs decently, and you use the truck for light hauling, but primarily just getting around.......why change it at all ? If it's a WANT versus a NEED, that's cool. Why not a warmed over 390 ? You don't need different motor mounts....your transmission bellhousing will mate.....the trucks gearing is likely right on.......and FE's are great torque monsters !!!