I sided with bos only to betray them to the Institute. Hacked liberty prime to nuke the prydwyn. Apparently you can mortar it down?

Each of the factions have their own way of bringing down the Prydwen: the Minutemen bring it down with their artillery (after which they defend the castle from a BoS counter-attack) while the Railroad sneaks into it, plants explosives and blows it up after you and others leave Prydwen. You already know the Institute variant.