Hmm, that IS an interesting question Bryn. Hmm, personally, either the Minutemen, as they can form an actually functioning version of the NCR, where the settlements help eachother out. The other is the Institute, if the SS is benevolent when they become director. True, Synth Freedom will more or less be gone, which is one thing I despise about the Instituted, but their tech may help ,make the Commonwealth a bastion of technology and security. Imagine Courser police
Well, technically the best (according to me) is to become Minuteman general, do their questline up to reclaiming and rebuilding the fort, then go to the Institute, following the main questline and finish the game with them.
There is no actual conflict between the Institute and the Minuteman and thus such ending leaves you effectively as the leader of both factions. The Minuteman will continue to help people on the topside, supported by some Institute tech that you will leak them and under your leadership the Institute can slowly become less secretive and more helpful while still retaining the concept of scientific advancement.