Changing trains late at night in an unfamiliar city can be quite stressful and challenging. If you were to take one train, I’d recommend taking the Narita Express to Shibuya and then catch a taxi. Shibuya and Shimokitazawa aren’t right next to each other so it will cost about 2,000yen I would guess. Taxis can usually take 4 people no problem, but it depends how much luggage you have. If you have 4 really large suitcases, you’ll have trouble fitting in a single taxi. Also, you could try one of the new type taxis that look like London black cabs. The publicity says they have more luggage space, although I’m yet to catch one with luggage so I’m not sure how true this is.
Good luck! Btw, Shimo is one of my favourite Tokyo neighbourhoods - good choice!