No, a standard shipping container would be large enough for a surface to air missile. Anything with that much range would be a surface to surface missile and not suitable for taking out AF1.
I was thinking along the lines of a RIM-116 Rolling Airframe Missile (RAM). It is an IR homing missile with a ~6 mile range. (click for larger image)
This is a fire and forget missile that doesn't require any additional radar or command guidance.
If you are going to do something like this, KISS. Using a submarine to shoot down AF1 is a huge expense for a single shot at a plane that may not come within range. It also represents a much larger risk of being discovered and backtracked.
WWG1WGA
Garde la Foi, mes amis! Nous nous sommes les sauveurs de la République! Maintenant et Toujours!
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LonePalm, le Républicain du verre cassé (The Broken Glass Republican)
I only posed that question because, as I understand it, AF1 had rerouted northwards towards Alaska; presuming that was a missile fired from the environs of Whidbey Island, Puget Sound, on June 10, 2018, either they would have fired a long range missile or they fired at a decoy with a short range missile.
It was Q that posted the picture of the mystery sub, although I don't remember that he ever claimed that it shot the June 10 missile.
To set up a launch platform, other than a shipping container, on Whidbey Island - at least sparsely populated - seems unlikely, which adds credence to a surface ship or a submarine. Even a surface ship would attract some attention, unlike a submarine that could remain submerged until long after dark.
While I admit no expertise in this area, I cannot see Puget Sound as an ideal launching site nor the channels on either side of Whidbey Island as a place I would want to get trapped with hostility in a submarine. As you say, It also represents a much larger risk of being discovered and backtracked.
Still, there seems little doubt that what rose into the sky that night from Puget Sound was a missile.