It comes down to personal preference and how well one handles a sleepless night. For me, it's not necessarily how much time in a lie-flat, arrival time at the destination and how I'll feel upon arrival. With a 35" inseam, I just can't sleep in Y anymore. I'll happily take the shorter route in Y on the westbound daytime flight, but not for the redeye. Starting my vacation stiff, sore, and unrested sets me up for a rough first couple days. Time away from work is precious, and those days are just too valuable to me.

The only way to arrive in NAP early the next day is connecting to AA780 PHL-NAP, but both J and W are basically full. All other routings arrive in the evening. Since OP has already stated intention to upgrade, realistically, it will involve avoiding PHL-NAP or BOS-LHR. This means 2 connections, or flying into FCO then taking a train - also 2 connections. At any rate, arrival in NAP is mid to late evening.

Since OP wants to apply a mileage upgrade, I'd personally connect to AA104 with J wide open, enjoy 3 hours lounge hopping at JFK, a few hours stretching the legs walking around London, then arrival to NAP around bedtime. If I was still on my 20's when I could take a Y cabin redeye in stride and I had 3 fewer orthopedic surgeries under my belt, I'd go with the shortest routing all day.