Thanks for the input everyone.
Daysleeper: I'd be interested to hear how long you had to transfer in Dublin? Current flights I am looking at would arrive in Dublin at 09:30 and then leave for JFK at 10:50, leaving 1h 20m to transfer and pre-clear. I guess with the flight arriving domestically, if you haven't cleared US customs you ain't flying! This would get us in to JFK at 13:20 which gives us a lot of the Thursday at our disposal.
There is an alternative flight via Dublin which would leave 3h 30m to transfer and pre-clear but that doesn't arrive until 18:45 so I would probably rather just fly direct and take the hit at JFK. Aer Lingus also have an option which allows for 3h 30m in Dublin but that is in to Newark, and I know nothing about getting from Newark to Manhattan.
There's too many variables when going to NYC! I should just have taken her somewhere easy, like Dublin! :P